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Reduce the benchmarking scope, remove Daniel's commented components, add conda ARM recipe
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‎Clustering_conda.yml‎

Lines changed: 10 additions & 96 deletions
Original file line numberDiff line numberDiff line change
@@ -169,16 +169,16 @@ stages:
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parameters:
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# - values: ["--method", "FCPS_AdaptiveDensityPeak"] # not in conda
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- values: ["--method", "FCPS_Minimax", "--seed", 2]
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- values: ["--method", "FCPS_MinEnergy", "--seed", 2]
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- values: ["--method", "FCPS_HDBSCAN_2", "--seed", 2]
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- values: ["--method", "FCPS_HDBSCAN_4", "--seed", 2]
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- values: ["--method", "FCPS_HDBSCAN_8", "--seed", 2]
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- values: ["--method", "FCPS_Diana", "--seed", 2]
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- values: ["--method", "FCPS_Fanny", "--seed", 2]
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- values: ["--method", "FCPS_Hardcl", "--seed", 2]
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- values: ["--method", "FCPS_Softcl", "--seed", 2]
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- values: ["--method", "FCPS_Clara", "--seed", 2]
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- values: ["--method", "FCPS_PAM", "--seed", 2]
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# - values: ["--method", "FCPS_MinEnergy", "--seed", 2]
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# - values: ["--method", "FCPS_HDBSCAN_2", "--seed", 2]
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# - values: ["--method", "FCPS_HDBSCAN_4", "--seed", 2]
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# - values: ["--method", "FCPS_HDBSCAN_8", "--seed", 2]
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# - values: ["--method", "FCPS_Diana", "--seed", 2]
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# - values: ["--method", "FCPS_Fanny", "--seed", 2]
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# - values: ["--method", "FCPS_Hardcl", "--seed", 2]
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# - values: ["--method", "FCPS_Softcl", "--seed", 2]
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# - values: ["--method", "FCPS_Clara", "--seed", 2]
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# - values: ["--method", "FCPS_PAM", "--seed", 2]
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inputs:
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- entries:
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- data.matrix
@@ -214,89 +214,3 @@ stages:
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outputs:
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- id: metrics.scores
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path: "{input}/{stage}/{module}/{params}/{dataset}.scores.gz"
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# ## daniel's data ###########################################################################
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# - id: danielsdata
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# modules:
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# - id: iris_manual
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# name: "Iris Dataset"
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# software_environment: "sklearn"
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# repository:
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# url: https://github.com/omnibenchmark-example/iris.git
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# commit: 47c63f0
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# - id: penguins
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# name: "Penguins Dataset"
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# software_environment: "sklearn"
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# repository:
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# url: https://github.com/omnibenchmark-example/penguins.git
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# commit: 9032478
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# outputs:
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# - id: data.features
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# path: "{input}/{stage}/{module}/{params}/{dataset}.features.csv"
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# - id: data.labels
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# path: "{input}/{stage}/{module}/{params}/{dataset}.labels.csv"
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# ## daniel's distances ########################################################################
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# - id: distances
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# modules:
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# - id: D1
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# software_environment: "sklearn"
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# parameters:
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# - values: ["--measure", "cosine"]
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# - values: ["--measure", "euclidean"]
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# - values: ["--measure", "manhattan"]
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# - values: ["--measure", "chebyshev"]
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# repository:
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# url: https://github.com/omnibenchmark-example/distance.git
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# commit: dd99d4f
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# inputs:
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# - entries:
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# - data.features
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# outputs:
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# - id: distances
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# path: "{input}/{stage}/{module}/{params}/{dataset}.distances.csv"
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# ## daniel's methods ###################################################################
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# - id: danielmethods
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# modules:
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# - id: kmeans
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# software_environment: "sklearn"
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# repository:
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# url: https://github.com/omnibenchmark-example/kmeans.git
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# commit: 049c8b1
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# - id: ward
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# software_environment: "R"
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# repository:
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# url: https://github.com/omnibenchmark-example/ward.git
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# commit: 976e3f3
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# inputs:
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# - entries:
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# - distances
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# outputs:
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# - id: methods.clusters
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# path: "{input}/{stage}/{module}/{params}/{dataset}.clusters.csv"
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# ## daniel's metrics ###################################################################
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# - id: danielsmetrics
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# modules:
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# - id: ari
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# software_environment: "R"
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# repository:
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# url: https://github.com/omnibenchmark-example/ari.git
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# commit: 72708f0
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# - id: accuracy
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# software_environment: "R"
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# repository:
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# url: https://github.com/omnibenchmark-example/accuracy.git
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# commit: e26b32f
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# inputs:
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# - entries:
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# - methods.clusters
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# - data.labels
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# outputs:
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# - id: metrics.mapping
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# path: "{input}/{stage}/{module}/{params}/{dataset}.metrics.txt"

‎Clustering_envmodules.yml‎

Lines changed: 10 additions & 96 deletions
Original file line numberDiff line numberDiff line change
@@ -172,16 +172,16 @@ stages:
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parameters:
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# - values: ["--method", "FCPS_AdaptiveDensityPeak"] # not in conda
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- values: ["--method", "FCPS_Minimax", "--seed", 2]
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- values: ["--method", "FCPS_MinEnergy", "--seed", 2]
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- values: ["--method", "FCPS_HDBSCAN_2", "--seed", 2]
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- values: ["--method", "FCPS_HDBSCAN_4", "--seed", 2]
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- values: ["--method", "FCPS_HDBSCAN_8", "--seed", 2]
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- values: ["--method", "FCPS_Diana", "--seed", 2]
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- values: ["--method", "FCPS_Fanny", "--seed", 2]
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- values: ["--method", "FCPS_Hardcl", "--seed", 2]
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- values: ["--method", "FCPS_Softcl", "--seed", 2]
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- values: ["--method", "FCPS_Clara", "--seed", 2]
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- values: ["--method", "FCPS_PAM", "--seed", 2]
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# - values: ["--method", "FCPS_MinEnergy", "--seed", 2]
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# - values: ["--method", "FCPS_HDBSCAN_2", "--seed", 2]
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# - values: ["--method", "FCPS_HDBSCAN_4", "--seed", 2]
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# - values: ["--method", "FCPS_HDBSCAN_8", "--seed", 2]
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# - values: ["--method", "FCPS_Diana", "--seed", 2]
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# - values: ["--method", "FCPS_Fanny", "--seed", 2]
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# - values: ["--method", "FCPS_Hardcl", "--seed", 2]
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# - values: ["--method", "FCPS_Softcl", "--seed", 2]
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# - values: ["--method", "FCPS_Clara", "--seed", 2]
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# - values: ["--method", "FCPS_PAM", "--seed", 2]
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inputs:
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- entries:
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- data.matrix
@@ -217,89 +217,3 @@ stages:
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outputs:
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- id: metrics.scores
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path: "{input}/{stage}/{module}/{params}/{dataset}.scores.gz"
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# ## daniel's data ###########################################################################
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# - id: danielsdata
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# modules:
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# - id: iris_manual
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# name: "Iris Dataset"
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# software_environment: "sklearn"
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# repository:
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# url: https://github.com/omnibenchmark-example/iris.git
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# commit: 47c63f0
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# - id: penguins
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# name: "Penguins Dataset"
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# software_environment: "sklearn"
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# repository:
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# url: https://github.com/omnibenchmark-example/penguins.git
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# commit: 9032478
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# outputs:
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# - id: data.features
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# path: "{input}/{stage}/{module}/{params}/{dataset}.features.csv"
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# - id: data.labels
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# path: "{input}/{stage}/{module}/{params}/{dataset}.labels.csv"
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# ## daniel's distances ########################################################################
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# - id: distances
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# modules:
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# - id: D1
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# software_environment: "sklearn"
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# parameters:
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# - values: ["--measure", "cosine"]
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# - values: ["--measure", "euclidean"]
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# - values: ["--measure", "manhattan"]
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# - values: ["--measure", "chebyshev"]
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# repository:
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# url: https://github.com/omnibenchmark-example/distance.git
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# commit: dd99d4f
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# inputs:
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# - entries:
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# - data.features
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# outputs:
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# - id: distances
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# path: "{input}/{stage}/{module}/{params}/{dataset}.distances.csv"
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# ## daniel's methods ###################################################################
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# - id: danielmethods
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# modules:
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# - id: kmeans
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# software_environment: "sklearn"
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# repository:
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# url: https://github.com/omnibenchmark-example/kmeans.git
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# commit: 049c8b1
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# - id: ward
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# software_environment: "R"
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# repository:
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# url: https://github.com/omnibenchmark-example/ward.git
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# commit: 976e3f3
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# inputs:
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# - entries:
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# - distances
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# outputs:
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# - id: methods.clusters
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# path: "{input}/{stage}/{module}/{params}/{dataset}.clusters.csv"
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# ## daniel's metrics ###################################################################
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# - id: danielsmetrics
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# modules:
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# - id: ari
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# software_environment: "R"
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# repository:
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# url: https://github.com/omnibenchmark-example/ari.git
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# commit: 72708f0
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# - id: accuracy
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# software_environment: "R"
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# repository:
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# url: https://github.com/omnibenchmark-example/accuracy.git
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# commit: e26b32f
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# inputs:
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# - entries:
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# - methods.clusters
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# - data.labels
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# outputs:
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# - id: metrics.mapping
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# path: "{input}/{stage}/{module}/{params}/{dataset}.metrics.txt"

‎Clustering_oras.yml‎

Lines changed: 10 additions & 96 deletions
Original file line numberDiff line numberDiff line change
@@ -170,16 +170,16 @@ stages:
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parameters:
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# - values: ["--method", "FCPS_AdaptiveDensityPeak"] # not in conda
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- values: ["--method", "FCPS_Minimax", "--seed", 2]
173-
- values: ["--method", "FCPS_MinEnergy", "--seed", 2]
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- values: ["--method", "FCPS_HDBSCAN_2", "--seed", 2]
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- values: ["--method", "FCPS_HDBSCAN_4", "--seed", 2]
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- values: ["--method", "FCPS_HDBSCAN_8", "--seed", 2]
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- values: ["--method", "FCPS_Diana", "--seed", 2]
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- values: ["--method", "FCPS_Fanny", "--seed", 2]
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- values: ["--method", "FCPS_Hardcl", "--seed", 2]
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- values: ["--method", "FCPS_Softcl", "--seed", 2]
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- values: ["--method", "FCPS_Clara", "--seed", 2]
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- values: ["--method", "FCPS_PAM", "--seed", 2]
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# - values: ["--method", "FCPS_MinEnergy", "--seed", 2]
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# - values: ["--method", "FCPS_HDBSCAN_2", "--seed", 2]
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# - values: ["--method", "FCPS_HDBSCAN_4", "--seed", 2]
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# - values: ["--method", "FCPS_HDBSCAN_8", "--seed", 2]
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# - values: ["--method", "FCPS_Diana", "--seed", 2]
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# - values: ["--method", "FCPS_Fanny", "--seed", 2]
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# - values: ["--method", "FCPS_Hardcl", "--seed", 2]
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# - values: ["--method", "FCPS_Softcl", "--seed", 2]
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# - values: ["--method", "FCPS_Clara", "--seed", 2]
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# - values: ["--method", "FCPS_PAM", "--seed", 2]
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inputs:
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- entries:
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- data.matrix
@@ -215,89 +215,3 @@ stages:
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outputs:
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- id: metrics.scores
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path: "{input}/{stage}/{module}/{params}/{dataset}.scores.gz"
218-
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# ## daniel's data ###########################################################################
220-
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# - id: danielsdata
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# modules:
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# - id: iris_manual
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# name: "Iris Dataset"
225-
# software_environment: "sklearn"
226-
# repository:
227-
# url: https://github.com/omnibenchmark-example/iris.git
228-
# commit: 47c63f0
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# - id: penguins
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# name: "Penguins Dataset"
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# software_environment: "sklearn"
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# repository:
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# url: https://github.com/omnibenchmark-example/penguins.git
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# commit: 9032478
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# outputs:
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# - id: data.features
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# path: "{input}/{stage}/{module}/{params}/{dataset}.features.csv"
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# - id: data.labels
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# path: "{input}/{stage}/{module}/{params}/{dataset}.labels.csv"
240-
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# ## daniel's distances ########################################################################
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# - id: distances
244-
# modules:
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# - id: D1
246-
# software_environment: "sklearn"
247-
# parameters:
248-
# - values: ["--measure", "cosine"]
249-
# - values: ["--measure", "euclidean"]
250-
# - values: ["--measure", "manhattan"]
251-
# - values: ["--measure", "chebyshev"]
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# repository:
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# url: https://github.com/omnibenchmark-example/distance.git
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# commit: dd99d4f
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# inputs:
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# - entries:
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# - data.features
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# outputs:
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# - id: distances
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# path: "{input}/{stage}/{module}/{params}/{dataset}.distances.csv"
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# ## daniel's methods ###################################################################
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# - id: danielmethods
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# modules:
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# - id: kmeans
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# software_environment: "sklearn"
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# repository:
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# url: https://github.com/omnibenchmark-example/kmeans.git
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# commit: 049c8b1
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# - id: ward
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# software_environment: "R"
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# repository:
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# url: https://github.com/omnibenchmark-example/ward.git
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# commit: 976e3f3
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# inputs:
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# - entries:
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# - distances
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# outputs:
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# - id: methods.clusters
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# path: "{input}/{stage}/{module}/{params}/{dataset}.clusters.csv"
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# ## daniel's metrics ###################################################################
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# - id: danielsmetrics
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# modules:
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# - id: ari
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# software_environment: "R"
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# repository:
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# url: https://github.com/omnibenchmark-example/ari.git
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# commit: 72708f0
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# - id: accuracy
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# software_environment: "R"
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# repository:
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# url: https://github.com/omnibenchmark-example/accuracy.git
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# commit: e26b32f
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# inputs:
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# - entries:
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# - methods.clusters
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# - data.labels
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# outputs:
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# - id: metrics.mapping
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# path: "{input}/{stage}/{module}/{params}/{dataset}.metrics.txt"

‎envs/clustbench_arm.yml‎

Lines changed: 18 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,18 @@
1+
name: fcps
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channels:
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- conda-forge
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- https://repo.prefix.dev/almost-conductor
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- r
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- nodefaults
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dependencies:
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- conda-forge::python=3.12.6
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- conda-forge::r-base>=4.0
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- r-fcps=1.3.4
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- r-datavisualizations==1.3.3
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- r-cclust==0.6.26
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- r-energy==1.7-12
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- r-protoclust==1.6.4
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- conda-forge::r-argparse==2.2.5
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- conda-forge::r-dbscan=1.2.2
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- conda-forge::r-cluster==2.1.8
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- conda-forge::r-mclust==6.1.1

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