run: unilateral base graph TI

- no risks or prevalences
- only transmission btw LNLs II, III and IV

README.md

@@ -9,31 +9,24 @@ node4["enhance"]
 node5["evaluate"]
 node6["join"]
 node7["plot-corner"]
-node8["predict-prevalences"]
-node9["predict-risks"]
-node10["sampling"]
-node11["remote"]
+node8["sampling"]
+node9["remote"]
 node1-->node6
-node1-->node11
+node1-->node9
 node2-->node6
-node2-->node11
+node2-->node9
 node3-->node5
 node3-->node8
-node3-->node10
-node3-->node11
+node3-->node9
 node4-->node3
-node4-->node11
-node5-->node11
+node4-->node9
+node5-->node9
 node6-->node4
-node6-->node11
-node7-->node11
-node8-->node11
-node9-->node11
-node10-->node5
-node10-->node7
-node10-->node8
-node10-->node9
-node10-->node11
+node6-->node9
+node7-->node9
+node8-->node5
+node8-->node7
+node8-->node9
 ```
 
 We are researchers in the field of medical physics and want to predict how cancer in the head & neck region spreads through the lymphatic system.
@@ -240,7 +233,7 @@ If there are still unanswered questions regarding this work, don't hesitate to :
 [zenodo]: https://zenodo.org
 [releases]: https://github.com/rmnldwg/lynference/releases
 
-[up-button]: https://img.shields.io/badge/%E2%96%B2-back%20to%20top-lightgrey
+[up-button]: https://dabuttonfactory.com/button.png?t=back+to+top&f=Roboto-Bold&ts=15&tc=eef&hp=16&vp=5&c=6&bgt=unicolored&bgc=89a
 
 ## References
 

dag.md

@@ -7,29 +7,22 @@ flowchart TD
 	node5["evaluate"]
 	node6["join"]
 	node7["plot-corner"]
-	node8["predict-prevalences"]
-	node9["predict-risks"]
-	node10["sampling"]
-	node11["remote"]
+	node8["sampling"]
+	node9["remote"]
 	node1-->node6
-	node1-->node11
+	node1-->node9
 	node2-->node6
-	node2-->node11
+	node2-->node9
 	node3-->node5
 	node3-->node8
-	node3-->node10
-	node3-->node11
+	node3-->node9
 	node4-->node3
-	node4-->node11
-	node5-->node11
+	node4-->node9
+	node5-->node9
 	node6-->node4
-	node6-->node11
-	node7-->node11
-	node8-->node11
-	node9-->node11
-	node10-->node5
-	node10-->node7
-	node10-->node8
-	node10-->node9
-	node10-->node11
+	node6-->node9
+	node7-->node9
+	node8-->node5
+	node8-->node7
+	node8-->node9
 ```

dvc.lock

@@ -5,8 +5,8 @@ stages:
       \ >> dag.md\n"
     outs:
     - path: dag.md
-      md5: 0e102d9fef8528a0f1c9237a88585990
-      size: 627
+      md5: c3fa8afe3eac35019e335d63e7b6c131
+      size: 480
   mermaid-png:
     cmd: ./node_modules/.bin/mmdc -i dag.md -o dag.png && mv dag-1.png dag.png
     deps:
@@ -21,39 +21,39 @@ stages:
     cmd: pip freeze | grep -v "pkg_resources" > frozen.txt
     outs:
     - path: frozen.txt
-      md5: 788305a20dff989f85af7228a8e30b44
-      size: 2361
+      md5: 53adf09f26be04ab8b13e0773ef5b28c
+      size: 2382
   pipeline:
     cmd: dvc repro pipeline/dvc.yaml
   remote:
     cmd: "rm -rf ../lynference.dvc && mkdir ../lynference.dvc && dvc remote add --force\
       \ local ../lynference.dvc && dvc push -r local\n"
     deps:
     - path: ./data
-      md5: b6a1468f7105288a63444dcfa78a182d.dir
-      size: 1236427
+      md5: 3a41b6c4c183d8b57e3dc60cd1d1ae91.dir
+      size: 1092093
       nfiles: 8
     - path: ./models
-      md5: b9368a7d1b1d30246694a99ee9e619df.dir
-      size: 5929824
-      nfiles: 3
+      md5: 55d558452b577fe937eaa6f9997c6808.dir
+      size: 38190520
+      nfiles: 1
     - path: ./plots
-      md5: 645e4fd6a927081b6b61af6ceb23eeb9.dir
-      size: 42998255
-      nfiles: 4
+      md5: 75d3337f0ed1d7862dc94a9d6a37e81f.dir
+      size: 4338558
+      nfiles: 5
     - path: metrics.json
-      md5: 9a71a3a0152ef8617045600221edef4b
-      size: 92
+      md5: ae7394fe35c6b2b7669081cbde141485
+      size: 159
   mermaid-readme:
     cmd: cat dag.md | sed 's/^/3i/' | sed -f- README.template > README.md
     deps:
     - path: README.template
       md5: b4774a95f1c7a06c5d29b202de91e28a
       size: 10765
     - path: dag.md
-      md5: 0e102d9fef8528a0f1c9237a88585990
-      size: 627
+      md5: c3fa8afe3eac35019e335d63e7b6c131
+      size: 480
     outs:
     - path: README.md
-      md5: 6a7e55c53c13bc5aaf1dceae5f188370
-      size: 11307
+      md5: 0b3deff99b7dbbfc3918fa2ac7b317f9
+      size: 11220

frozen.txt

@@ -36,22 +36,22 @@ diskcache==5.4.0
 distro==1.7.0
 dpath==2.0.6
 dulwich==0.20.46
-dvc==2.30.0
-dvc-azure==2.20.4
-dvc-data==0.17.1
+dvc==2.35.2
+dvc-azure==2.20.5
+dvc-data==0.28.0
 dvc-gdrive==2.19.0
 dvc-http==2.27.2
-dvc-objects==0.7.0
-dvc-render==0.0.12
-dvc-task==0.1.3
-dvclive==0.10.0
+dvc-objects==0.14.0
+dvc-render==0.0.14
+dvc-task==0.1.6
+dvclive==1.0.1
 emcee==3.1.2
 filelock==3.8.0
 flatten-dict==0.4.2
 flufl.lock==7.1
 fonttools==4.37.1
 frozenlist==1.3.1
-fsspec==2022.7.1
+fsspec==2022.11.0
 funcy==1.17
 future==0.18.2
 gitdb==4.0.9
@@ -68,13 +68,13 @@ hydra-core==1.2.0
 idna==3.3
 importlib-resources==5.9.0
 isodate==0.6.1
-iterative-telemetry==0.0.5
+iterative-telemetry==0.0.6
 jmespath==1.0.1
 kiwisolver==1.4.4
 knack==0.10.0
 kombu==5.2.4
 lymph-model==0.4.3
-lyscripts==0.5.10
+lyscripts==0.6.6
 matplotlib==3.5.3
 msal==1.18.0
 msal-extensions==1.0.0
@@ -112,11 +112,12 @@ PyYAML==6.0
 requests==2.28.1
 requests-oauthlib==1.3.1
 rich==12.5.1
+rich_argparse==0.5.0
 rsa==4.9
 ruamel.yaml==0.17.21
 ruamel.yaml.clib==0.2.6
 scipy==1.9.1
-scmrepo==0.1.1
+scmrepo==0.1.3
 shortuuid==1.0.9
 shtab==1.5.5
 six==1.16.0

params.yaml

@@ -18,8 +18,8 @@ graph:
     primary: [I, II, III, IV, V, VII]
   lnl:
     I: []
-    II: [I, III, V]
-    III: [IV, V]
+    II: [III]
+    III: [IV]
     IV: []
     V: []
     VII: []
@@ -30,7 +30,7 @@ model:
   first_binom_prob: 0.3         # defines shape of time prior of first T-stage
   max_t: 10                     # max number of time steps to evolve system
   t_stages: [early, late]       # T-stages to consider in the data
-  class: MidlineBilateral       # model class to use (see `lymph-model` docs)
+  class: Unilateral             # model class to use (see `lymph-model` docs)
   # keyword arguments to pass to the model constructor
   kwargs:
     base_symmetric: false
@@ -94,8 +94,25 @@ inference_modalities:
 sampling:
   walkers_per_dim: 20           # num of parallel walkers per parameter space dimension
   burnin: 1000                  # burn-in steps to discard
-  nsteps: 50                    # do this many serious steps per sampling round
-  thin_by: 5                    # draw this many samples for one step in `nsteps`
+  nsteps: 20                    # do this many serious steps per sampling round
+  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
+  - 0.004115226337448558
+  - 0.010240000000000003
+  - 0.022132674897119342
+  - 0.043151275720164604
+  - 0.07775999999999998
+  - 0.13168724279835387
+  - 0.21208362139917689
+  - 0.3276800000000001
+  - 0.48894551440329226
+  - 0.708245596707819
+  - 1.0
   # only used when sampling until convergence
   kwargs:
     max_steps: 20000
@@ -107,34 +124,7 @@ sampling:
 # RISKS:
 # Every entry in this array defines a scenario for which the stage
 # `predict-risk` will compute the risks, given a set of samples
-risks:
-- name: contra/III/N0/late/ext
-  involvement:
-    contra: {III: true}
-  given_diagnosis:
-    ipsi:   {I: false, II: false, III: false, IV: false, V: false, VII: false}
-    contra: {I: false, II: false, III: false, IV: false, V: false, VII: false}
-  given_diagnosis_spsn: [0.76, 0.81]
-  t_stage: late
-  midline_extension: true
-- name: contra/III/ipsi-IIandIII/late/noext
-  involvement:
-    contra: {III: true}
-  given_diagnosis:
-    ipsi:   {I: false, II: true , III: true , IV: false, V: false, VII: false}
-    contra: {I: false, II: false, III: false, IV: false, V: false, VII: false}
-  given_diagnosis_spsn: [0.76, 0.81]
-  t_stage: late
-  midline_extension: false
-- name: contra/III/ipsi-IIandIII/late/ext
-  involvement:
-    contra: {III: true}
-  given_diagnosis:
-    ipsi:   {I: false, II: true , III: true , IV: false, V: false, VII: false}
-    contra: {I: false, II: false, III: false, IV: false, V: false, VII: false}
-  given_diagnosis_spsn: [0.76, 0.81]
-  t_stage: late
-  midline_extension: true
+risks: []
 
 
 ########################################################################################
@@ -144,30 +134,4 @@ risks:
 # prevalence of a certain pattern of involvement for a defined
 # diagnostic modality. It can, however, be compared to the prevalence
 # in the data.
-prevalences:
-# ipsilateral
-- name: ipsi/IInotI/early
-  pattern:
-    ipsi: {I: false, II: true}
-  modality: max_llh
-  modality_spsn: [1.0, 1.0]
-  t_stage: early
-- name: ipsi/IInotI/late
-  pattern:
-    ipsi: {I: false, II: true}
-  modality: max_llh
-  modality_spsn: [1.0, 1.0]
-  t_stage: late
-
-- name: ipsi/IIandIII/early
-  pattern:
-    ipsi: {II: true, III: true}
-  modality: max_llh
-  modality_spsn: [1.0, 1.0]
-  t_stage: early
-- name: ipsi/IIandIII/late
-  pattern:
-    ipsi: {II: true, III: true}
-  modality: max_llh
-  modality_spsn: [1.0, 1.0]
-  t_stage: late
+prevalences: []