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Running MARK03 - Post Log Prob Fix #160

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merged 2 commits into from
Aug 31, 2023
Merged

Running MARK03 - Post Log Prob Fix #160

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1838f3f
setup mark03
gordonkoehn Aug 30, 2023
643a06e
remove MP§
gordonkoehn Aug 31, 2023
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8 changes: 4 additions & 4 deletions workflows/mark03.smk
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Original file line number Diff line number Diff line change
Expand Up @@ -17,14 +17,14 @@ from pyggdrasil.tree_inference import CellSimulationId, TreeType, TreeId, McmcCo

#####################
# Environment variables
DATADIR = "../data"
#DATADIR = "/cluster/work/bewi/members/gkoehn/data"
#DATADIR = "../data"
DATADIR = "/cluster/work/bewi/members/gkoehn/data"

#####################
experiment = "mark03"

# Metrics: Distances / Similarity Measure to use
metrics = ["MP3", "AD", "log_prob", "DL"] # <-- configure distances here
metrics = ["AD", "log_prob", "DL"] # also MP3 <-- configure distances here

#####################
# Error Parameters
Expand Down Expand Up @@ -64,7 +64,7 @@ CS_seed = 42 # <-- configure cell simulation seed here
#####################
# True Tree Parameters
tree_types = ["r"] # <-- configure tree type here ["r","s","d"]
tree_seeds = [42] # <-- configure tree seed here
tree_seeds = [42,34] # <-- configure tree seed here

#####################
#####################
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6 changes: 3 additions & 3 deletions workflows/tree_inference.smk
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Expand Up @@ -19,9 +19,9 @@ from pyggdrasil.tree_inference import (
###############################################
## Relative path from DATADIR to the repo root

#REPODIR = "/cluster/work/bewi/members/gkoehn/repos/PYggdrasil"
REPODIR = ".."
#DATADIR = "/cluster/work/bewi/members/gkoehn/data"
REPODIR = "/cluster/work/bewi/members/gkoehn/repos/PYggdrasil"
#REPODIR = ".."
DATADIR = "/cluster/work/bewi/members/gkoehn/data"

###############################################

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