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@@ -33,3 +33,322 @@ saved_model/**/* filter=lfs diff=lfs merge=lfs -text
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+outputs/eval_mean_ntv2/run_data=ntv2_70_hg38_mean,model=encoder/levenshtein_vs_entropy_predicted.pdf filter=lfs diff=lfs merge=lfs -text
+outputs/eval_mean_ntv2/run_data=ntv2_70_hg38_mean,model=encoder/levenshtein_vs_entropy_true.pdf filter=lfs diff=lfs merge=lfs -text
+outputs/eval_mean_ntv2/run_data=ntv2_70_hg38_mean,model=knn/levenshtein_vs_entropy_predicted.pdf filter=lfs diff=lfs merge=lfs -text
+outputs/eval_mean_ntv2/run_data=ntv2_70_hg38_mean,model=knn/levenshtein_vs_entropy_true.pdf filter=lfs diff=lfs merge=lfs -text
+outputs/eval_mean_ntv2/run_data=ntv2_70_hg38_mean,model=resnet/levenshtein_vs_entropy_predicted.pdf filter=lfs diff=lfs merge=lfs -text
+outputs/eval_mean_ntv2/run_data=ntv2_70_hg38_mean,model=resnet/levenshtein_vs_entropy_true.pdf filter=lfs diff=lfs merge=lfs -text
+outputs/eval_mean_ntv2/run_data=ntv2_80_hg38_mean,model=decoder/levenshtein_vs_entropy_predicted.pdf filter=lfs diff=lfs merge=lfs -text
+outputs/eval_mean_ntv2/run_data=ntv2_80_hg38_mean,model=decoder/levenshtein_vs_entropy_true.pdf filter=lfs diff=lfs merge=lfs -text
+outputs/eval_mean_ntv2/run_data=ntv2_80_hg38_mean,model=encoder/levenshtein_vs_entropy_predicted.pdf filter=lfs diff=lfs merge=lfs -text
+outputs/eval_mean_ntv2/run_data=ntv2_80_hg38_mean,model=encoder/levenshtein_vs_entropy_true.pdf filter=lfs diff=lfs merge=lfs -text
+outputs/eval_mean_ntv2/run_data=ntv2_80_hg38_mean,model=knn/levenshtein_vs_entropy_predicted.pdf filter=lfs diff=lfs merge=lfs -text
+outputs/eval_mean_ntv2/run_data=ntv2_80_hg38_mean,model=knn/levenshtein_vs_entropy_true.pdf filter=lfs diff=lfs merge=lfs -text
+outputs/eval_mean_ntv2/run_data=ntv2_80_hg38_mean,model=resnet/levenshtein_vs_entropy_predicted.pdf filter=lfs diff=lfs merge=lfs -text
+outputs/eval_mean_ntv2/run_data=ntv2_80_hg38_mean,model=resnet/levenshtein_vs_entropy_true.pdf filter=lfs diff=lfs merge=lfs -text
+outputs/eval_mean_ntv2/run_data=ntv2_90_hg38_mean,model=decoder/levenshtein_vs_entropy_predicted.pdf filter=lfs diff=lfs merge=lfs -text
+outputs/eval_mean_ntv2/run_data=ntv2_90_hg38_mean,model=decoder/levenshtein_vs_entropy_true.pdf filter=lfs diff=lfs merge=lfs -text
+outputs/eval_mean_ntv2/run_data=ntv2_90_hg38_mean,model=encoder/levenshtein_vs_entropy_predicted.pdf filter=lfs diff=lfs merge=lfs -text
+outputs/eval_mean_ntv2/run_data=ntv2_90_hg38_mean,model=encoder/levenshtein_vs_entropy_true.pdf filter=lfs diff=lfs merge=lfs -text
+outputs/eval_mean_ntv2/run_data=ntv2_90_hg38_mean,model=knn/levenshtein_vs_entropy_predicted.pdf filter=lfs diff=lfs merge=lfs -text
+outputs/eval_mean_ntv2/run_data=ntv2_90_hg38_mean,model=knn/levenshtein_vs_entropy_true.pdf filter=lfs diff=lfs merge=lfs -text
+outputs/eval_mean_ntv2/run_data=ntv2_90_hg38_mean,model=resnet/levenshtein_vs_entropy_predicted.pdf filter=lfs diff=lfs merge=lfs -text
+outputs/eval_mean_ntv2/run_data=ntv2_90_hg38_mean,model=resnet/levenshtein_vs_entropy_true.pdf filter=lfs diff=lfs merge=lfs -text
+outputs/eval_per_token_dnabert2_100_hg38_per_token/accuracy_metrics.png filter=lfs diff=lfs merge=lfs -text
+outputs/eval_per_token_dnabert2_100_hg38_per_token/confusion_matrix.png filter=lfs diff=lfs merge=lfs -text
+outputs/eval_per_token_dnabert2_100_hg38_per_token/levenshtein_vs_entropy_predicted.pdf filter=lfs diff=lfs merge=lfs -text
+outputs/eval_per_token_dnabert2_100_hg38_per_token/levenshtein_vs_entropy_predicted.png filter=lfs diff=lfs merge=lfs -text
+outputs/eval_per_token_dnabert2_100_hg38_per_token/levenshtein_vs_entropy_true.pdf filter=lfs diff=lfs merge=lfs -text
+outputs/eval_per_token_dnabert2_100_hg38_per_token/levenshtein_vs_entropy_true.png filter=lfs diff=lfs merge=lfs -text
+outputs/eval_per_token_dnabert2_100_hg38_per_token/levenshtein_vs_repetitiveness_predicted.png filter=lfs diff=lfs merge=lfs -text
+outputs/eval_per_token_dnabert2_100_hg38_per_token/levenshtein_vs_repetitiveness_true.png filter=lfs diff=lfs merge=lfs -text
+outputs/eval_per_token_dnabert2_100_hg38_per_token/per_position_accuracy.png filter=lfs diff=lfs merge=lfs -text
+outputs/eval_per_token_evo2_100_hg38_per_token/accuracy_metrics.png filter=lfs diff=lfs merge=lfs -text
+outputs/eval_per_token_evo2_100_hg38_per_token/confusion_matrix.png filter=lfs diff=lfs merge=lfs -text
+outputs/eval_per_token_evo2_100_hg38_per_token/levenshtein_vs_entropy_predicted.pdf filter=lfs diff=lfs merge=lfs -text
+outputs/eval_per_token_evo2_100_hg38_per_token/levenshtein_vs_entropy_predicted.png filter=lfs diff=lfs merge=lfs -text
+outputs/eval_per_token_evo2_100_hg38_per_token/levenshtein_vs_entropy_true.pdf filter=lfs diff=lfs merge=lfs -text
+outputs/eval_per_token_evo2_100_hg38_per_token/levenshtein_vs_entropy_true.png filter=lfs diff=lfs merge=lfs -text
+outputs/eval_per_token_evo2_100_hg38_per_token/levenshtein_vs_repetitiveness_predicted.png filter=lfs diff=lfs merge=lfs -text
+outputs/eval_per_token_evo2_100_hg38_per_token/levenshtein_vs_repetitiveness_true.png filter=lfs diff=lfs merge=lfs -text
+outputs/eval_per_token_evo2_100_hg38_per_token/per_position_accuracy.png filter=lfs diff=lfs merge=lfs -text
+outputs/eval_per_token_ntv2_100_hg38_per_token/accuracy_metrics.png filter=lfs diff=lfs merge=lfs -text
+outputs/eval_per_token_ntv2_100_hg38_per_token/confusion_matrix.png filter=lfs diff=lfs merge=lfs -text
+outputs/eval_per_token_ntv2_100_hg38_per_token/levenshtein_vs_entropy_predicted.pdf filter=lfs diff=lfs merge=lfs -text
+outputs/eval_per_token_ntv2_100_hg38_per_token/levenshtein_vs_entropy_predicted.png filter=lfs diff=lfs merge=lfs -text
+outputs/eval_per_token_ntv2_100_hg38_per_token/levenshtein_vs_entropy_true.pdf filter=lfs diff=lfs merge=lfs -text
+outputs/eval_per_token_ntv2_100_hg38_per_token/levenshtein_vs_entropy_true.png filter=lfs diff=lfs merge=lfs -text
+outputs/eval_per_token_ntv2_100_hg38_per_token/levenshtein_vs_repetitiveness_predicted.png filter=lfs diff=lfs merge=lfs -text
+outputs/eval_per_token_ntv2_100_hg38_per_token/levenshtein_vs_repetitiveness_true.png filter=lfs diff=lfs merge=lfs -text
+outputs/eval_per_token_ntv2_100_hg38_per_token/per_position_accuracy.png filter=lfs diff=lfs merge=lfs -text

outputs/analysis_mean_dnabert2/data=dnabert2_100_hg38_mean/.hydra/config.yaml

@@ -0,0 +1,25 @@
+data:
+  shuffle: true
+  mean: true
+  train_csv: data/train_dnabert2_100_hg38.h5
+  val_csv: data/val_dnabert2_100_hg38.h5
+  test_csv: data/test_dnabert2_100_hg38.h5
+  embedding_dim: 768
+  seq_length: 100
+  skip_sha256_check: false
+  normalization_method: standard
+  subset_fraction: null
+  tokenizer:
+    type: huggingface
+    model_name: zhihan1996/DNABERT-2-117M
+  checkpoint: zhihan1996/DNABERT-2-117M
+  train_sha256: 1BA1E85A5BB2028D566189A70E75CD46E3BC162F2AEA21FDE586E46A603297C0
+  val_sha256: 7A2CB9CEB4C87A2DB32EFCAC0D8CE5C46940385516FCC4B433A92378F8176C1F
+  test_sha256: 96508011F6AB76EE519438563BB5D5F4BEE607433A6042F3C4323D790845D0B8
+splits: null
+comparison_groups: []
+seed: 42
+subsample: 2000
+n_neighbors: 15
+min_dist: 0.1
+perplexity: 30

outputs/analysis_mean_dnabert2/data=dnabert2_100_hg38_mean/.hydra/hydra.yaml

@@ -0,0 +1,158 @@
+hydra:
+  run:
+    dir: outputs/embedding_analysis-${now:%Y-%m-%d-%H-%M-%S}
+  sweep:
+    dir: outputs/analysis_mean_dnabert2
+    subdir: ${hydra.job.override_dirname}
+  launcher:
+    _target_: hydra._internal.core_plugins.basic_launcher.BasicLauncher
+  sweeper:
+    _target_: hydra._internal.core_plugins.basic_sweeper.BasicSweeper
+    max_batch_size: null
+    params: null
+  help:
+    app_name: ${hydra.job.name}
+    header: '${hydra.help.app_name} is powered by Hydra.
+
+      '
+    footer: 'Powered by Hydra (https://hydra.cc)
+
+      Use --hydra-help to view Hydra specific help
+
+      '
+    template: '${hydra.help.header}
+
+      == Configuration groups ==
+
+      Compose your configuration from those groups (group=option)
+
+
+      $APP_CONFIG_GROUPS
+
+
+      == Config ==
+
+      Override anything in the config (foo.bar=value)
+
+
+      $CONFIG
+
+
+      ${hydra.help.footer}
+
+      '
+  hydra_help:
+    template: 'Hydra (${hydra.runtime.version})
+
+      See https://hydra.cc for more info.
+
+
+      == Flags ==
+
+      $FLAGS_HELP
+
+
+      == Configuration groups ==
+
+      Compose your configuration from those groups (For example, append hydra/job_logging=disabled
+      to command line)
+
+
+      $HYDRA_CONFIG_GROUPS
+
+
+      Use ''--cfg hydra'' to Show the Hydra config.
+
+      '
+    hydra_help: ???
+  hydra_logging:
+    version: 1
+    formatters:
+      simple:
+        format: '[%(asctime)s][HYDRA] %(message)s'
+    handlers:
+      console:
+        class: logging.StreamHandler
+        formatter: simple
+        stream: ext://sys.stdout
+    root:
+      level: INFO
+      handlers:
+      - console
+    loggers:
+      logging_example:
+        level: DEBUG
+    disable_existing_loggers: false
+  job_logging:
+    version: 1
+    formatters:
+      simple:
+        format: '%(asctime)s | %(levelname)s | %(message)s'
+    handlers:
+      console:
+        class: logging.StreamHandler
+        formatter: simple
+        stream: ext://sys.stdout
+      file:
+        class: logging.FileHandler
+        formatter: simple
+        filename: ${hydra.runtime.output_dir}/${hydra.job.name}.log
+    root:
+      level: INFO
+      handlers:
+      - console
+      - file
+    disable_existing_loggers: false
+  env: {}
+  mode: MULTIRUN
+  searchpath: []
+  callbacks: {}
+  output_subdir: .hydra
+  overrides:
+    hydra:
+    - hydra.sweep.dir=outputs/analysis_mean_dnabert2
+    - hydra.sweep.subdir=${hydra.job.override_dirname}
+    - hydra.mode=MULTIRUN
+    task:
+    - data=dnabert2_100_hg38_mean
+  job:
+    name: embedding_analysis_mean
+    chdir: true
+    override_dirname: data=dnabert2_100_hg38_mean
+    id: '13'
+    num: 13
+    config_name: embedding_analysis
+    env_set: {}
+    env_copy: []
+    config:
+      override_dirname:
+        kv_sep: '='
+        item_sep: ','
+        exclude_keys: []
+  runtime:
+    version: 1.3.2
+    version_base: '1.3'
+    cwd: /weka/pfeifer/ppu738/DNA_Foundation_Models_Inversion_Attack_Benchmark
+    config_sources:
+    - path: hydra.conf
+      schema: pkg
+      provider: hydra
+    - path: /weka/pfeifer/ppu738/DNA_Foundation_Models_Inversion_Attack_Benchmark/conf
+      schema: file
+      provider: main
+    - path: ''
+      schema: structured
+      provider: schema
+    output_dir: /weka/pfeifer/ppu738/DNA_Foundation_Models_Inversion_Attack_Benchmark/outputs/analysis_mean_dnabert2/data=dnabert2_100_hg38_mean
+    choices:
+      data: dnabert2_100_hg38_mean
+      hydra/env: default
+      hydra/callbacks: null
+      hydra/job_logging: default
+      hydra/hydra_logging: default
+      hydra/hydra_help: default
+      hydra/help: default
+      hydra/sweeper: basic
+      hydra/launcher: basic
+      hydra/output: default
+  verbose: false

outputs/analysis_mean_dnabert2/data=dnabert2_100_hg38_mean/.hydra/overrides.yaml

@@ -0,0 +1 @@
+- data=dnabert2_100_hg38_mean

outputs/analysis_mean_dnabert2/data=dnabert2_100_hg38_mean/norm_euclidean_dists.npy

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:38dd5b0cb70139ab4b0f14b518bfb49f70973bad4f40b6d1990f4f26d374a598
+size 15992128

outputs/analysis_mean_dnabert2/data=dnabert2_100_hg38_mean/stats.json

@@ -0,0 +1,17 @@
+{
+    "dataset": "dnabert2_100_hg38_mean",
+    "n_samples": 2000,
+    "avg_seq_len": 100.0,
+    "max_euclidean_dist": 19.052656173706055,
+    "embedding_dim": 768,
+    "spearman_corr_cosine": 0.1127012282239274,
+    "spearman_corr_euclidean": 0.10046659770255992,
+    "entropy_mean": 1.9011786971278106,
+    "entropy_std": 0.08234891934301493,
+    "entropy_min": 0.7780113035465377,
+    "entropy_max": 2.0,
+    "repetitiveness_mean": 0.2547371134020619,
+    "repetitiveness_std": 0.0802358025446897,
+    "frac_low_entropy_lt1.5": 0.002,
+    "frac_low_kmer_lt0.3": 0.7945
+}

outputs/analysis_mean_dnabert2/data=dnabert2_10_hg38_mean/.hydra/config.yaml

@@ -0,0 +1,25 @@
+data:
+  shuffle: true
+  mean: true
+  train_csv: data/train_dnabert2_10_hg38.h5
+  val_csv: data/val_dnabert2_10_hg38.h5
+  test_csv: data/test_dnabert2_10_hg38.h5
+  embedding_dim: 768
+  seq_length: 10
+  skip_sha256_check: false
+  normalization_method: standard
+  subset_fraction: null
+  tokenizer:
+    type: huggingface
+    model_name: zhihan1996/DNABERT-2-117M
+  checkpoint: zhihan1996/DNABERT-2-117M
+  train_sha256: 82B0E69676797C8892BDA60CAD731768401DD1C05511C43261D654EFEDDE1294
+  val_sha256: 50211F172BC486394131B3164B7893F862104D902D09039DD5F1C8A17277BE3B
+  test_sha256: 2908120E92F21E92EE8E39501AA680C78E813B301DD18774E961474E8AEF6F9E
+splits: null
+comparison_groups: []
+seed: 42
+subsample: 2000
+n_neighbors: 15
+min_dist: 0.1
+perplexity: 30

outputs/analysis_mean_dnabert2/data=dnabert2_10_hg38_mean/.hydra/hydra.yaml

@@ -0,0 +1,158 @@
+hydra:
+  run:
+    dir: outputs/embedding_analysis-${now:%Y-%m-%d-%H-%M-%S}
+  sweep:
+    dir: outputs/analysis_mean_dnabert2
+    subdir: ${hydra.job.override_dirname}
+  launcher:
+    _target_: hydra._internal.core_plugins.basic_launcher.BasicLauncher
+  sweeper:
+    _target_: hydra._internal.core_plugins.basic_sweeper.BasicSweeper
+    max_batch_size: null
+    params: null
+  help:
+    app_name: ${hydra.job.name}
+    header: '${hydra.help.app_name} is powered by Hydra.
+
+      '
+    footer: 'Powered by Hydra (https://hydra.cc)
+
+      Use --hydra-help to view Hydra specific help
+
+      '
+    template: '${hydra.help.header}
+
+      == Configuration groups ==
+
+      Compose your configuration from those groups (group=option)
+
+
+      $APP_CONFIG_GROUPS
+
+
+      == Config ==
+
+      Override anything in the config (foo.bar=value)
+
+
+      $CONFIG
+
+
+      ${hydra.help.footer}
+
+      '
+  hydra_help:
+    template: 'Hydra (${hydra.runtime.version})
+
+      See https://hydra.cc for more info.
+
+
+      == Flags ==
+
+      $FLAGS_HELP
+
+
+      == Configuration groups ==
+
+      Compose your configuration from those groups (For example, append hydra/job_logging=disabled
+      to command line)
+
+
+      $HYDRA_CONFIG_GROUPS
+
+
+      Use ''--cfg hydra'' to Show the Hydra config.
+
+      '
+    hydra_help: ???
+  hydra_logging:
+    version: 1
+    formatters:
+      simple:
+        format: '[%(asctime)s][HYDRA] %(message)s'
+    handlers:
+      console:
+        class: logging.StreamHandler
+        formatter: simple
+        stream: ext://sys.stdout
+    root:
+      level: INFO
+      handlers:
+      - console
+    loggers:
+      logging_example:
+        level: DEBUG
+    disable_existing_loggers: false
+  job_logging:
+    version: 1
+    formatters:
+      simple:
+        format: '%(asctime)s | %(levelname)s | %(message)s'
+    handlers:
+      console:
+        class: logging.StreamHandler
+        formatter: simple
+        stream: ext://sys.stdout
+      file:
+        class: logging.FileHandler
+        formatter: simple
+        filename: ${hydra.runtime.output_dir}/${hydra.job.name}.log
+    root:
+      level: INFO
+      handlers:
+      - console
+      - file
+    disable_existing_loggers: false
+  env: {}
+  mode: MULTIRUN
+  searchpath: []
+  callbacks: {}
+  output_subdir: .hydra
+  overrides:
+    hydra:
+    - hydra.sweep.dir=outputs/analysis_mean_dnabert2
+    - hydra.sweep.subdir=${hydra.job.override_dirname}
+    - hydra.mode=MULTIRUN
+    task:
+    - data=dnabert2_10_hg38_mean
+  job:
+    name: embedding_analysis_mean
+    chdir: true
+    override_dirname: data=dnabert2_10_hg38_mean
+    id: '0'
+    num: 0
+    config_name: embedding_analysis
+    env_set: {}
+    env_copy: []
+    config:
+      override_dirname:
+        kv_sep: '='
+        item_sep: ','
+        exclude_keys: []
+  runtime:
+    version: 1.3.2
+    version_base: '1.3'
+    cwd: /weka/pfeifer/ppu738/DNA_Foundation_Models_Inversion_Attack_Benchmark
+    config_sources:
+    - path: hydra.conf
+      schema: pkg
+      provider: hydra
+    - path: /weka/pfeifer/ppu738/DNA_Foundation_Models_Inversion_Attack_Benchmark/conf
+      schema: file
+      provider: main
+    - path: ''
+      schema: structured
+      provider: schema
+    output_dir: /weka/pfeifer/ppu738/DNA_Foundation_Models_Inversion_Attack_Benchmark/outputs/analysis_mean_dnabert2/data=dnabert2_10_hg38_mean
+    choices:
+      data: dnabert2_10_hg38_mean
+      hydra/env: default
+      hydra/callbacks: null
+      hydra/job_logging: default
+      hydra/hydra_logging: default
+      hydra/hydra_help: default
+      hydra/help: default
+      hydra/sweeper: basic
+      hydra/launcher: basic
+      hydra/output: default
+  verbose: false

outputs/analysis_mean_dnabert2/data=dnabert2_10_hg38_mean/.hydra/overrides.yaml

@@ -0,0 +1 @@
+- data=dnabert2_10_hg38_mean

outputs/analysis_mean_dnabert2/data=dnabert2_10_hg38_mean/norm_euclidean_dists.npy

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:f6f10f052b7d9225fa0c34a9058969ad97c1e1477560d198e7b42a8c5c56ef24
+size 15992128

outputs/analysis_mean_dnabert2/data=dnabert2_10_hg38_mean/stats.json

@@ -0,0 +1,17 @@
+{
+    "dataset": "dnabert2_10_hg38_mean",
+    "n_samples": 2000,
+    "avg_seq_len": 10.0,
+    "max_euclidean_dist": 19.68452262878418,
+    "embedding_dim": 768,
+    "spearman_corr_cosine": 0.01537474849934102,
+    "spearman_corr_euclidean": 0.022368682806938916,
+    "entropy_mean": 1.7591126180042016,
+    "entropy_std": 0.1946674262191716,
+    "entropy_min": 0.46899559358928117,
+    "entropy_max": 1.970950594454669,
+    "repetitiveness_mean": 0.01092857142857143,
+    "repetitiveness_std": 0.04751965221820101,
+    "frac_low_entropy_lt1.5": 0.132,
+    "frac_low_kmer_lt0.3": 0.997
+}

outputs/analysis_mean_dnabert2/data=dnabert2_15_hg38_mean/.hydra/config.yaml

@@ -0,0 +1,25 @@
+data:
+  shuffle: true
+  mean: true
+  train_csv: data/train_dnabert2_15_hg38.h5
+  val_csv: data/val_dnabert2_15_hg38.h5
+  test_csv: data/test_dnabert2_15_hg38.h5
+  embedding_dim: 768
+  seq_length: 15
+  skip_sha256_check: false
+  normalization_method: standard
+  subset_fraction: null
+  tokenizer:
+    type: huggingface
+    model_name: zhihan1996/DNABERT-2-117M
+  checkpoint: zhihan1996/DNABERT-2-117M
+  train_sha256: 6E44A1CB5C3A8168669EF7311C401A2C29F4A1B18AF54F41E6CAB10F2997A4A2
+  val_sha256: B9D463B134D88D6DC7F992BBA09E8327AAF19B096A8AF1AF2687BDEB30630DE9
+  test_sha256: 7A0A461B9199DADE785581CA145C6960A210C10FF47559422FCD519A1215E00F
+splits: null
+comparison_groups: []
+seed: 42
+subsample: 2000
+n_neighbors: 15
+min_dist: 0.1
+perplexity: 30

outputs/analysis_mean_dnabert2/data=dnabert2_15_hg38_mean/.hydra/hydra.yaml

@@ -0,0 +1,158 @@
+hydra:
+  run:
+    dir: outputs/embedding_analysis-${now:%Y-%m-%d-%H-%M-%S}
+  sweep:
+    dir: outputs/analysis_mean_dnabert2
+    subdir: ${hydra.job.override_dirname}
+  launcher:
+    _target_: hydra._internal.core_plugins.basic_launcher.BasicLauncher
+  sweeper:
+    _target_: hydra._internal.core_plugins.basic_sweeper.BasicSweeper
+    max_batch_size: null
+    params: null
+  help:
+    app_name: ${hydra.job.name}
+    header: '${hydra.help.app_name} is powered by Hydra.
+
+      '
+    footer: 'Powered by Hydra (https://hydra.cc)
+
+      Use --hydra-help to view Hydra specific help
+
+      '
+    template: '${hydra.help.header}
+
+      == Configuration groups ==
+
+      Compose your configuration from those groups (group=option)
+
+
+      $APP_CONFIG_GROUPS
+
+
+      == Config ==
+
+      Override anything in the config (foo.bar=value)
+
+
+      $CONFIG
+
+
+      ${hydra.help.footer}
+
+      '
+  hydra_help:
+    template: 'Hydra (${hydra.runtime.version})
+
+      See https://hydra.cc for more info.
+
+
+      == Flags ==
+
+      $FLAGS_HELP
+
+
+      == Configuration groups ==
+
+      Compose your configuration from those groups (For example, append hydra/job_logging=disabled
+      to command line)
+
+
+      $HYDRA_CONFIG_GROUPS
+
+
+      Use ''--cfg hydra'' to Show the Hydra config.
+
+      '
+    hydra_help: ???
+  hydra_logging:
+    version: 1
+    formatters:
+      simple:
+        format: '[%(asctime)s][HYDRA] %(message)s'
+    handlers:
+      console:
+        class: logging.StreamHandler
+        formatter: simple
+        stream: ext://sys.stdout
+    root:
+      level: INFO
+      handlers:
+      - console
+    loggers:
+      logging_example:
+        level: DEBUG
+    disable_existing_loggers: false
+  job_logging:
+    version: 1
+    formatters:
+      simple:
+        format: '%(asctime)s | %(levelname)s | %(message)s'
+    handlers:
+      console:
+        class: logging.StreamHandler
+        formatter: simple
+        stream: ext://sys.stdout
+      file:
+        class: logging.FileHandler
+        formatter: simple
+        filename: ${hydra.runtime.output_dir}/${hydra.job.name}.log
+    root:
+      level: INFO
+      handlers:
+      - console
+      - file
+    disable_existing_loggers: false
+  env: {}
+  mode: MULTIRUN
+  searchpath: []
+  callbacks: {}
+  output_subdir: .hydra
+  overrides:
+    hydra:
+    - hydra.sweep.dir=outputs/analysis_mean_dnabert2
+    - hydra.sweep.subdir=${hydra.job.override_dirname}
+    - hydra.mode=MULTIRUN
+    task:
+    - data=dnabert2_15_hg38_mean
+  job:
+    name: embedding_analysis_mean
+    chdir: true
+    override_dirname: data=dnabert2_15_hg38_mean
+    id: '1'
+    num: 1
+    config_name: embedding_analysis
+    env_set: {}
+    env_copy: []
+    config:
+      override_dirname:
+        kv_sep: '='
+        item_sep: ','
+        exclude_keys: []
+  runtime:
+    version: 1.3.2
+    version_base: '1.3'
+    cwd: /weka/pfeifer/ppu738/DNA_Foundation_Models_Inversion_Attack_Benchmark
+    config_sources:
+    - path: hydra.conf
+      schema: pkg
+      provider: hydra
+    - path: /weka/pfeifer/ppu738/DNA_Foundation_Models_Inversion_Attack_Benchmark/conf
+      schema: file
+      provider: main
+    - path: ''
+      schema: structured
+      provider: schema
+    output_dir: /weka/pfeifer/ppu738/DNA_Foundation_Models_Inversion_Attack_Benchmark/outputs/analysis_mean_dnabert2/data=dnabert2_15_hg38_mean
+    choices:
+      data: dnabert2_15_hg38_mean
+      hydra/env: default
+      hydra/callbacks: null
+      hydra/job_logging: default
+      hydra/hydra_logging: default
+      hydra/hydra_help: default
+      hydra/help: default
+      hydra/sweeper: basic
+      hydra/launcher: basic
+      hydra/output: default
+  verbose: false

outputs/analysis_mean_dnabert2/data=dnabert2_15_hg38_mean/.hydra/overrides.yaml

@@ -0,0 +1 @@
+- data=dnabert2_15_hg38_mean

outputs/analysis_mean_dnabert2/data=dnabert2_15_hg38_mean/norm_euclidean_dists.npy

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:51a626e493be031f2b798291bfe848d266cc7e5202864682a38cb18fa95a152d
+size 15992128

outputs/analysis_mean_dnabert2/data=dnabert2_15_hg38_mean/stats.json

@@ -0,0 +1,17 @@
+{
+    "dataset": "dnabert2_15_hg38_mean",
+    "n_samples": 2000,
+    "avg_seq_len": 15.0,
+    "max_euclidean_dist": 20.000253677368164,
+    "embedding_dim": 768,
+    "spearman_corr_cosine": 0.0289325687280639,
+    "spearman_corr_euclidean": 0.028296070449735755,
+    "entropy_mean": 1.780084897107418,
+    "entropy_std": 0.1685190390474686,
+    "entropy_min": 0.9709505944546688,
+    "entropy_max": 1.9898980954642875,
+    "repetitiveness_mean": 0.03075,
+    "repetitiveness_std": 0.061114589547468574,
+    "frac_low_entropy_lt1.5": 0.068,
+    "frac_low_kmer_lt0.3": 0.9895
+}

outputs/analysis_mean_dnabert2/data=dnabert2_20_hg38_mean/.hydra/config.yaml

@@ -0,0 +1,25 @@
+data:
+  shuffle: true
+  mean: true
+  train_csv: data/train_dnabert2_20_hg38.h5
+  val_csv: data/val_dnabert2_20_hg38.h5
+  test_csv: data/test_dnabert2_20_hg38.h5
+  embedding_dim: 768
+  seq_length: 20
+  skip_sha256_check: false
+  normalization_method: standard
+  subset_fraction: null
+  tokenizer:
+    type: huggingface
+    model_name: zhihan1996/DNABERT-2-117M
+  checkpoint: zhihan1996/DNABERT-2-117M
+  train_sha256: 5498E19D30B944E1ABF640653EEB79013591DA44FE41254465C9F554F58934E1
+  val_sha256: 7AD9CEABFCF6CD0E5695F4FB7EA19B3B96DAF2675FE7BE1F5B0E941C54422CFE
+  test_sha256: 0875580F9E656311D9259B10E46E0DD3AD2D39F01F98400AB3E36022E58728FF
+splits: null
+comparison_groups: []
+seed: 42
+subsample: 2000
+n_neighbors: 15
+min_dist: 0.1
+perplexity: 30

outputs/analysis_mean_dnabert2/data=dnabert2_20_hg38_mean/.hydra/hydra.yaml

@@ -0,0 +1,158 @@
+hydra:
+  run:
+    dir: outputs/embedding_analysis-${now:%Y-%m-%d-%H-%M-%S}
+  sweep:
+    dir: outputs/analysis_mean_dnabert2
+    subdir: ${hydra.job.override_dirname}
+  launcher:
+    _target_: hydra._internal.core_plugins.basic_launcher.BasicLauncher
+  sweeper:
+    _target_: hydra._internal.core_plugins.basic_sweeper.BasicSweeper
+    max_batch_size: null
+    params: null
+  help:
+    app_name: ${hydra.job.name}
+    header: '${hydra.help.app_name} is powered by Hydra.
+
+      '
+    footer: 'Powered by Hydra (https://hydra.cc)
+
+      Use --hydra-help to view Hydra specific help
+
+      '
+    template: '${hydra.help.header}
+
+      == Configuration groups ==
+
+      Compose your configuration from those groups (group=option)
+
+
+      $APP_CONFIG_GROUPS
+
+
+      == Config ==
+
+      Override anything in the config (foo.bar=value)
+
+
+      $CONFIG
+
+
+      ${hydra.help.footer}
+
+      '
+  hydra_help:
+    template: 'Hydra (${hydra.runtime.version})
+
+      See https://hydra.cc for more info.
+
+
+      == Flags ==
+
+      $FLAGS_HELP
+
+
+      == Configuration groups ==
+
+      Compose your configuration from those groups (For example, append hydra/job_logging=disabled
+      to command line)
+
+
+      $HYDRA_CONFIG_GROUPS
+
+
+      Use ''--cfg hydra'' to Show the Hydra config.
+
+      '
+    hydra_help: ???
+  hydra_logging:
+    version: 1
+    formatters:
+      simple:
+        format: '[%(asctime)s][HYDRA] %(message)s'
+    handlers:
+      console:
+        class: logging.StreamHandler
+        formatter: simple
+        stream: ext://sys.stdout
+    root:
+      level: INFO
+      handlers:
+      - console
+    loggers:
+      logging_example:
+        level: DEBUG
+    disable_existing_loggers: false
+  job_logging:
+    version: 1
+    formatters:
+      simple:
+        format: '%(asctime)s | %(levelname)s | %(message)s'
+    handlers:
+      console:
+        class: logging.StreamHandler
+        formatter: simple
+        stream: ext://sys.stdout
+      file:
+        class: logging.FileHandler
+        formatter: simple
+        filename: ${hydra.runtime.output_dir}/${hydra.job.name}.log
+    root:
+      level: INFO
+      handlers:
+      - console
+      - file
+    disable_existing_loggers: false
+  env: {}
+  mode: MULTIRUN
+  searchpath: []
+  callbacks: {}
+  output_subdir: .hydra
+  overrides:
+    hydra:
+    - hydra.sweep.dir=outputs/analysis_mean_dnabert2
+    - hydra.sweep.subdir=${hydra.job.override_dirname}
+    - hydra.mode=MULTIRUN
+    task:
+    - data=dnabert2_20_hg38_mean
+  job:
+    name: embedding_analysis_mean
+    chdir: true
+    override_dirname: data=dnabert2_20_hg38_mean
+    id: '2'
+    num: 2
+    config_name: embedding_analysis
+    env_set: {}
+    env_copy: []
+    config:
+      override_dirname:
+        kv_sep: '='
+        item_sep: ','
+        exclude_keys: []
+  runtime:
+    version: 1.3.2
+    version_base: '1.3'
+    cwd: /weka/pfeifer/ppu738/DNA_Foundation_Models_Inversion_Attack_Benchmark
+    config_sources:
+    - path: hydra.conf
+      schema: pkg
+      provider: hydra
+    - path: /weka/pfeifer/ppu738/DNA_Foundation_Models_Inversion_Attack_Benchmark/conf
+      schema: file
+      provider: main
+    - path: ''
+      schema: structured
+      provider: schema
+    output_dir: /weka/pfeifer/ppu738/DNA_Foundation_Models_Inversion_Attack_Benchmark/outputs/analysis_mean_dnabert2/data=dnabert2_20_hg38_mean
+    choices:
+      data: dnabert2_20_hg38_mean
+      hydra/env: default
+      hydra/callbacks: null
+      hydra/job_logging: default
+      hydra/hydra_logging: default
+      hydra/hydra_help: default
+      hydra/help: default
+      hydra/sweeper: basic
+      hydra/launcher: basic
+      hydra/output: default
+  verbose: false

outputs/analysis_mean_dnabert2/data=dnabert2_20_hg38_mean/.hydra/overrides.yaml

@@ -0,0 +1 @@
+- data=dnabert2_20_hg38_mean

outputs/analysis_mean_dnabert2/data=dnabert2_20_hg38_mean/norm_euclidean_dists.npy

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:97b5d8e9b381ca3f4267724f31b0e243cac320bc1678ded9058ee655400e4bd2
+size 15992128