diff --git a/.github/workflows/cml.yaml b/.github/workflows/cml.yaml
index 92b815ae..b82d8888 100644
--- a/.github/workflows/cml.yaml
+++ b/.github/workflows/cml.yaml
@@ -21,21 +21,26 @@ jobs:
         with:
           python-version-file: ".python-version"
 
+      - name: Generate datasets and models
+        run: |
+          # Supervised game: Generate datasets and models
+          uv run proteingym-base list-datasets datasets | jq 'map(select(.name == "charge_ladder" or .name == "NEIME_2019")) | map({name: .name, input_filename: .input_filename})' | yq -p json -o json '. = {"datasets": .}' > benchmark/supervised/local/datasets.json
+          uv run proteingym-base list-models models | jq 'map(select(.name == "pls")) | map({name: .name, input_filename: .input_filename})' | yq -p json -o json '. = {"models": .}' > benchmark/supervised/local/models.json
+          
+          # Zero-shot game: Generate datasets and models
+          uv run proteingym-base list-datasets datasets | jq 'map(select(.name == "ranganathan")) | map({name: .name, input_filename: .input_filename})' | yq -p json -o json '. = {"datasets": .}' > benchmark/zero_shot/local/datasets.json
+          uv run proteingym-base list-models models | jq 'map(select(.name == "esm")) | map({name: .name, input_filename: .input_filename})' | yq -p json -o json '. = {"models": .}' > benchmark/zero_shot/local/models.json
+          
       - name: Run model validation
         env:
           repo_token: ${{ secrets.PERSONAL_ACCESS_TOKEN }}
-        run: |
-          # Configure PAT to git clone the private repo: proteingym-base
-          git config --global credential.helper store
-          echo "https://${{ secrets.USERNAME }}:${{ secrets.PERSONAL_ACCESS_TOKEN }}@github.com" > ~/.git-credentials
-          uv sync
-     
-          # Run DVC repro
-          echo "https://${{ secrets.USERNAME }}:${{ secrets.PERSONAL_ACCESS_TOKEN }}@github.com" > benchmark/supervised/git-auth.txt
-          echo "https://${{ secrets.USERNAME }}:${{ secrets.PERSONAL_ACCESS_TOKEN }}@github.com" > benchmark/zero_shot/git-auth.txt
+        run: | 
+          # Supervised game: Run DVC repro
           uv run dvc repro benchmark/supervised/local/dvc.yaml
+  
+          # Zero-shot game: Run DVC repro
           uv run dvc repro benchmark/zero_shot/local/dvc.yaml
-          
+
           # Create report with metrics
           # Pick one supervised model
           echo "✅ Supervised models have all passed validation." >> report.md
diff --git a/benchmark/supervised/local/default.yaml b/benchmark/supervised/local/default.yaml
new file mode 100644
index 00000000..239fc9eb
--- /dev/null
+++ b/benchmark/supervised/local/default.yaml
@@ -0,0 +1,3 @@
+output:
+  prediction: output
+  metric: metric
diff --git a/benchmark/supervised/local/dvc.lock b/benchmark/supervised/local/dvc.lock
deleted file mode 100644
index 5e1904ba..00000000
--- a/benchmark/supervised/local/dvc.lock
+++ /dev/null
@@ -1,97 +0,0 @@
-schema: '2.0'
-stages:
-  create_training_job@dataset0-model0:
-    cmd:
-    - docker build --build-arg GIT_CACHE_BUST=1 --secret id=git_auth,src=../git-auth.txt
-      -f ../../../models/pls/Dockerfile -t pls:latest ../../..
-    - docker run --rm -v $(realpath ../../../datasets):/datasets -v $(realpath ../../../models):/models
-      -v $(realpath output):/opt/ml/model pls:latest train --dataset-file /datasets/dummy/dataset.zip
-      --model-card-file /models/pls/README.md
-    - docker image prune -a -f
-    deps:
-    - path: ../../../datasets/dummy/dataset.zip
-      hash: md5
-      md5: 6efa993ab1d169974759032feae3f93c
-      size: 33985
-    - path: ../../../models/pls/Dockerfile
-      hash: md5
-      md5: 901a42e51cf4a14665099985ee9c30de
-      size: 1138
-    - path: ../../../models/pls/README.md
-      hash: md5
-      md5: 9fad88f2cb03369789d7143c7ee4844b
-      size: 837
-    - path: logs/setup.txt
-      hash: md5
-      md5: c861b0c201d5e28492f5dff8fab634f5
-      size: 26
-    outs:
-    - path: output/charge_ladder_pls.csv
-      hash: md5
-      md5: 2331ac53475416456e701ecdf6ee51b5
-      size: 13780
-  create_training_job@dataset1-model0:
-    cmd:
-    - docker build --build-arg GIT_CACHE_BUST=1 --secret id=git_auth,src=../git-auth.txt
-      -f ../../../models/pls/Dockerfile -t pls:latest ../../..
-    - docker run --rm -v $(realpath ../../../datasets):/datasets -v $(realpath ../../../models):/models
-      -v $(realpath output):/opt/ml/model pls:latest train --dataset-file /datasets/neime/dataset.zip
-      --model-card-file /models/pls/README.md
-    - docker image prune -a -f
-    deps:
-    - path: ../../../datasets/neime/dataset.zip
-      hash: md5
-      md5: 45524cd511a606635ea0ba0b84ce7b55
-      size: 8375
-    - path: ../../../models/pls/Dockerfile
-      hash: md5
-      md5: 901a42e51cf4a14665099985ee9c30de
-      size: 1138
-    - path: ../../../models/pls/README.md
-      hash: md5
-      md5: 9fad88f2cb03369789d7143c7ee4844b
-      size: 837
-    - path: logs/setup.txt
-      hash: md5
-      md5: c861b0c201d5e28492f5dff8fab634f5
-      size: 26
-    outs:
-    - path: output/neime_pls.csv
-      hash: md5
-      md5: 0ba5399bd48be7053fd80f12065daf08
-      size: 35028
-  calculate_metric@dataset0-model0:
-    cmd: uv run pg2-benchmark metric calc --output-path output/charge_ladder_pls.csv
-      --metric-path metric/charge_ladder_pls.csv
-    deps:
-    - path: output/charge_ladder_pls.csv
-      hash: md5
-      md5: 2331ac53475416456e701ecdf6ee51b5
-      size: 13780
-    outs:
-    - path: metric/charge_ladder_pls.csv
-      hash: md5
-      md5: 566553f3fe5f4eca170de4a58d60e007
-      size: 1457
-  calculate_metric@dataset1-model0:
-    cmd: uv run pg2-benchmark metric calc --output-path output/neime_pls.csv --metric-path
-      metric/neime_pls.csv
-    deps:
-    - path: output/neime_pls.csv
-      hash: md5
-      md5: 0ba5399bd48be7053fd80f12065daf08
-      size: 35028
-    outs:
-    - path: metric/neime_pls.csv
-      hash: md5
-      md5: 64464e0f19baeb76e4921e583a991427
-      size: 1623
-  setup:
-    cmd:
-    - mkdir -p logs output metric
-    - echo "Created local directories" > logs/setup.txt
-    outs:
-    - path: logs/setup.txt
-      hash: md5
-      md5: c861b0c201d5e28492f5dff8fab634f5
-      size: 26
diff --git a/benchmark/supervised/local/dvc.yaml b/benchmark/supervised/local/dvc.yaml
index 9d8839bc..78d18126 100644
--- a/benchmark/supervised/local/dvc.yaml
+++ b/benchmark/supervised/local/dvc.yaml
@@ -1,47 +1,32 @@
 vars:
-  - params.yaml
-
-  - datasets:
-    - name: charge_ladder
-      container_path: /datasets/dummy/dataset.zip
-      local_path: ../../../datasets/dummy/dataset.zip
-
-    - name: neime
-      container_path: /datasets/neime/dataset.zip
-      local_path: ../../../datasets/neime/dataset.zip
-
-  - models:
-    - name: pls
-      container_path: /models/pls/README.md
-      local_path: ../../../models/pls/README.md
-      dockerfile: ../../../models/pls/Dockerfile
+  - default.yaml
+  - datasets.json
+  - models.json
 
 stages:
 
   setup:
-    cmd: 
-      - mkdir -p logs ${destination.output_dir} ${destination.metric_dir}
+    cmd:
+      - mkdir -p logs ${output.prediction} ${output.metric}
       - echo "Created local directories" > logs/setup.txt
     outs:
       - logs/setup.txt
-    
+
   create_training_job:
-    matrix: 
+    matrix:
       dataset: ${datasets}
       model: ${models}
 
-    cmd: 
-      - docker build --build-arg GIT_CACHE_BUST=${git.git_cache_bust} --secret id=git_auth,src=../git-auth.txt -f ${item.model.dockerfile} -t ${item.model.name}:latest ../../..
-      - docker run --rm -v $(realpath ${source.datasets_dir}):/datasets -v $(realpath ${source.models_dir}):/models -v $(realpath ${destination.output_dir}):/opt/ml/model ${item.model.name}:latest train --dataset-file ${item.dataset.container_path} --model-card-file ${item.model.container_path}
+    cmd:
+      - docker build -f $(dirname ${item.model.input_filename})/Dockerfile -t ${item.model.name}:latest $(dirname ${item.model.input_filename})
+      - docker run --rm -v $(realpath ${item.dataset.input_filename}):/$(basename ${item.dataset.input_filename}) -v $(realpath ${item.model.input_filename}):/$(basename ${item.model.input_filename}) -v $(realpath ${output.prediction}):/opt/ml/model ${item.model.name}:latest train --dataset-file /$(basename ${item.dataset.input_filename}) --model-card-file /$(basename ${item.model.input_filename})
       - docker image prune -a -f
-    
     deps:
       - logs/setup.txt
-      - ${item.dataset.local_path}
-      - ${item.model.local_path}
-      - ${item.model.dockerfile}
+      - ${item.dataset.input_filename}
+      - ${item.model.input_filename}
     outs:
-      - ${destination.output_dir}/${item.dataset.name}_${item.model.name}.csv:
+      - ${output.prediction}/${item.dataset.name}_${item.model.name}.csv:
           cache: true
 
   calculate_metric:
@@ -49,9 +34,9 @@ stages:
       dataset: ${datasets}
       model: ${models}
 
-    cmd: uv run proteingym-benchmark metric calc --output-path ${destination.output_dir}/${item.dataset.name}_${item.model.name}.csv --metric-path ${destination.metric_dir}/${item.dataset.name}_${item.model.name}.csv
+    cmd: uv run proteingym-benchmark metric calc --output-path ${output.prediction}/${item.dataset.name}_${item.model.name}.csv --metric-path ${output.metric}/${item.dataset.name}_${item.model.name}.csv
     deps:
-      - ${destination.output_dir}/${item.dataset.name}_${item.model.name}.csv
+      - ${output.prediction}/${item.dataset.name}_${item.model.name}.csv
     outs:
-      - ${destination.metric_dir}/${item.dataset.name}_${item.model.name}.csv:
-          cache: true
\ No newline at end of file
+      - ${output.metric}/${item.dataset.name}_${item.model.name}.csv:
+          cache: true
diff --git a/benchmark/supervised/local/params.yaml b/benchmark/supervised/local/params.yaml
deleted file mode 100644
index f62b55a2..00000000
--- a/benchmark/supervised/local/params.yaml
+++ /dev/null
@@ -1,10 +0,0 @@
-git:
-  git_cache_bust: 1
-
-source:
-  datasets_dir: ../../../datasets
-  models_dir: ../../../models
-  
-destination:
-  output_dir: output
-  metric_dir: metric
diff --git a/benchmark/zero_shot/local/default.yaml b/benchmark/zero_shot/local/default.yaml
new file mode 100644
index 00000000..239fc9eb
--- /dev/null
+++ b/benchmark/zero_shot/local/default.yaml
@@ -0,0 +1,3 @@
+output:
+  prediction: output
+  metric: metric
diff --git a/benchmark/zero_shot/local/dvc.lock b/benchmark/zero_shot/local/dvc.lock
deleted file mode 100644
index f813dfc0..00000000
--- a/benchmark/zero_shot/local/dvc.lock
+++ /dev/null
@@ -1,54 +0,0 @@
-schema: '2.0'
-stages:
-  create_training_job@dataset0-model0:
-    cmd:
-    - docker build --build-arg GIT_CACHE_BUST=1 --secret id=git_auth,src=../git-auth.txt
-      -f ../../../models/esm/Dockerfile -t esm:latest ../../..
-    - docker run --rm -v $(realpath ../../../datasets):/datasets -v $(realpath ../../../models):/models
-      -v $(realpath output):/opt/ml/model esm:latest train --dataset-file /datasets/ranganathan/dataset.zip
-      --model-card-file /models/esm/README.md
-    - docker image prune -a -f
-    deps:
-    - path: ../../../datasets/ranganathan/dataset.zip
-      hash: md5
-      md5: b7c8410bc7d34c92e8d11d8b0064fbc7
-      size: 39040
-    - path: ../../../models/esm/Dockerfile
-      hash: md5
-      md5: 7f13567daf55f157ab05f23602a1f53e
-      size: 1138
-    - path: ../../../models/esm/README.md
-      hash: md5
-      md5: 10e1bc81ab111c1023db5b3df2f77e0f
-      size: 1741
-    - path: logs/setup.txt
-      hash: md5
-      md5: c861b0c201d5e28492f5dff8fab634f5
-      size: 26
-    outs:
-    - path: output/ranganathan_esm.csv
-      hash: md5
-      md5: 39b2dea9bd44e696936e6b3e4f1a4a4c
-      size: 195883
-  calculate_metric@dataset0-model0:
-    cmd: uv run pg2-benchmark metric calc --output-path output/ranganathan_esm.csv
-      --metric-path metric/ranganathan_esm.csv
-    deps:
-    - path: output/ranganathan_esm.csv
-      hash: md5
-      md5: 39b2dea9bd44e696936e6b3e4f1a4a4c
-      size: 195883
-    outs:
-    - path: metric/ranganathan_esm.csv
-      hash: md5
-      md5: f38bb057ff25591c67c5985a58af8d1f
-      size: 1588
-  setup:
-    cmd:
-    - mkdir -p logs output metric
-    - echo "Created local directories" > logs/setup.txt
-    outs:
-    - path: logs/setup.txt
-      hash: md5
-      md5: c861b0c201d5e28492f5dff8fab634f5
-      size: 26
diff --git a/benchmark/zero_shot/local/dvc.yaml b/benchmark/zero_shot/local/dvc.yaml
index 3f5d520d..78d18126 100644
--- a/benchmark/zero_shot/local/dvc.yaml
+++ b/benchmark/zero_shot/local/dvc.yaml
@@ -1,53 +1,42 @@
 vars:
-  - params.yaml
-  
-  - datasets:
-    - name: ranganathan
-      container_path: /datasets/ranganathan/dataset.zip
-      local_path: ../../../datasets/ranganathan/dataset.zip
-
-  - models:
-    - name: esm
-      container_path: /models/esm/README.md
-      local_path: ../../../models/esm/README.md
-      dockerfile: ../../../models/esm/Dockerfile
+  - default.yaml
+  - datasets.json
+  - models.json
 
 stages:
 
   setup:
-    cmd: 
-      - mkdir -p logs ${destination.output_dir} ${destination.metric_dir}
+    cmd:
+      - mkdir -p logs ${output.prediction} ${output.metric}
       - echo "Created local directories" > logs/setup.txt
     outs:
       - logs/setup.txt
 
   create_training_job:
-    matrix: 
+    matrix:
       dataset: ${datasets}
       model: ${models}
-    
-    cmd: 
-      - docker build --build-arg GIT_CACHE_BUST=${git.git_cache_bust} --secret id=git_auth,src=../git-auth.txt -f ${item.model.dockerfile} -t ${item.model.name}:latest ../../..
-      - docker run --rm -v $(realpath ${source.datasets_dir}):/datasets -v $(realpath ${source.models_dir}):/models -v $(realpath ${destination.output_dir}):/opt/ml/model ${item.model.name}:latest train --dataset-file ${item.dataset.container_path} --model-card-file ${item.model.container_path}
-      - docker image prune -a -f
 
+    cmd:
+      - docker build -f $(dirname ${item.model.input_filename})/Dockerfile -t ${item.model.name}:latest $(dirname ${item.model.input_filename})
+      - docker run --rm -v $(realpath ${item.dataset.input_filename}):/$(basename ${item.dataset.input_filename}) -v $(realpath ${item.model.input_filename}):/$(basename ${item.model.input_filename}) -v $(realpath ${output.prediction}):/opt/ml/model ${item.model.name}:latest train --dataset-file /$(basename ${item.dataset.input_filename}) --model-card-file /$(basename ${item.model.input_filename})
+      - docker image prune -a -f
     deps:
       - logs/setup.txt
-      - ${item.dataset.local_path}
-      - ${item.model.local_path}
-      - ${item.model.dockerfile}
+      - ${item.dataset.input_filename}
+      - ${item.model.input_filename}
     outs:
-      - ${destination.output_dir}/${item.dataset.name}_${item.model.name}.csv:
+      - ${output.prediction}/${item.dataset.name}_${item.model.name}.csv:
           cache: true
 
   calculate_metric:
     matrix: 
       dataset: ${datasets}
       model: ${models}
-    
-    cmd: uv run proteingym-benchmark metric calc --output-path ${destination.output_dir}/${item.dataset.name}_${item.model.name}.csv --metric-path ${destination.metric_dir}/${item.dataset.name}_${item.model.name}.csv
+
+    cmd: uv run proteingym-benchmark metric calc --output-path ${output.prediction}/${item.dataset.name}_${item.model.name}.csv --metric-path ${output.metric}/${item.dataset.name}_${item.model.name}.csv
     deps:
-      - ${destination.output_dir}/${item.dataset.name}_${item.model.name}.csv
+      - ${output.prediction}/${item.dataset.name}_${item.model.name}.csv
     outs:
-      - ${destination.metric_dir}/${item.dataset.name}_${item.model.name}.csv:
-          cache: true
\ No newline at end of file
+      - ${output.metric}/${item.dataset.name}_${item.model.name}.csv:
+          cache: true
diff --git a/benchmark/zero_shot/local/params.yaml b/benchmark/zero_shot/local/params.yaml
deleted file mode 100644
index 5a3d12ef..00000000
--- a/benchmark/zero_shot/local/params.yaml
+++ /dev/null
@@ -1,10 +0,0 @@
-git:
-  git_cache_bust: 1
-
-source:
-  datasets_dir: ../../../datasets
-  models_dir: ../../../models
-  
-destination:
-  output_dir: output
-  metric_dir: metric
\ No newline at end of file
diff --git a/datasets/NEIME_2019.pgdata b/datasets/NEIME_2019.pgdata
new file mode 100644
index 00000000..aa4ff9d9
Binary files /dev/null and b/datasets/NEIME_2019.pgdata differ
diff --git a/datasets/charge_ladder.pgdata b/datasets/charge_ladder.pgdata
new file mode 100644
index 00000000..2480b348
Binary files /dev/null and b/datasets/charge_ladder.pgdata differ
diff --git a/datasets/dummy/dataset.zip b/datasets/dummy/dataset.zip
deleted file mode 100644
index ab53aeae..00000000
Binary files a/datasets/dummy/dataset.zip and /dev/null differ
diff --git a/datasets/neime/dataset.zip b/datasets/neime/dataset.zip
deleted file mode 100644
index 697be805..00000000
Binary files a/datasets/neime/dataset.zip and /dev/null differ
diff --git a/datasets/ranganathan.pgdata b/datasets/ranganathan.pgdata
new file mode 100644
index 00000000..36aa1d74
Binary files /dev/null and b/datasets/ranganathan.pgdata differ
diff --git a/datasets/ranganathan/dataset.zip b/datasets/ranganathan/dataset.zip
deleted file mode 100644
index f8a6fc51..00000000
Binary files a/datasets/ranganathan/dataset.zip and /dev/null differ
diff --git a/dist/.gitignore b/dist/.gitignore
new file mode 100644
index 00000000..f59ec20a
--- /dev/null
+++ b/dist/.gitignore
@@ -0,0 +1 @@
+*
\ No newline at end of file
diff --git a/dist/proteingym_base-0.1.0b1-py3-none-any.whl b/dist/proteingym_base-0.1.0b1-py3-none-any.whl
new file mode 100644
index 00000000..664b7237
Binary files /dev/null and b/dist/proteingym_base-0.1.0b1-py3-none-any.whl differ
diff --git a/models/esm/Dockerfile b/models/esm/Dockerfile
index 606313ec..100a5085 100644
--- a/models/esm/Dockerfile
+++ b/models/esm/Dockerfile
@@ -11,8 +11,7 @@ COPY dist/proteingym*.whl dist/
 # Copy and install dependencies
 COPY README.md README.md
 COPY pyproject.toml pyproject.toml
-RUN uv sync --no-cache
-
 COPY src/ src/
+RUN uv sync --no-cache
 
 ENTRYPOINT ["uv", "run", "esm"]
diff --git a/models/esm/dist/.gitignore b/models/esm/dist/.gitignore
new file mode 100644
index 00000000..f59ec20a
--- /dev/null
+++ b/models/esm/dist/.gitignore
@@ -0,0 +1 @@
+*
\ No newline at end of file
diff --git a/models/esm/dist/proteingym_base-0.1.0b1-py3-none-any.whl b/models/esm/dist/proteingym_base-0.1.0b1-py3-none-any.whl
new file mode 100644
index 00000000..664b7237
Binary files /dev/null and b/models/esm/dist/proteingym_base-0.1.0b1-py3-none-any.whl differ
diff --git a/models/esm/pyproject.toml b/models/esm/pyproject.toml
index 421ff6ea..00ed3906 100644
--- a/models/esm/pyproject.toml
+++ b/models/esm/pyproject.toml
@@ -7,7 +7,6 @@ requires-python = ">=3.12"
 dependencies = [
     "typer~=0.16.0",
     "proteingym-base[biopython]",
-    "proteingym-benchmark",
     "fair-esm~=2.0.0",
     "torch~=2.7.1",
     "bio~=1.8.0",
@@ -23,12 +22,11 @@ requires = ["hatchling"]
 build-backend = "hatchling.build"
 
 [tool.uv.sources]
-# TODO: After proteingym-base and proteingym-benchmark are public repositories, below reference can be updated
+# TODO: After proteingym-base is public repositories, below reference can be updated
 proteingym-base = { path = "dist/proteingym_base-0.1.0b1-py3-none-any.whl" }
-proteingym-benchmark = { path = "dist/proteingym_benchmark-0.1.0b1-py3-none-any.whl" }
 
 [tool.hatch.build.targets.wheel]
-packages = ["src/"]
+packages = ["src/proteingym"]
 
 [tool.ruff]
 line-length = 88
diff --git a/models/esm/src/proteingym/models/esm/__main__.py b/models/esm/src/proteingym/models/esm/__main__.py
index 9979e604..eecd64e8 100644
--- a/models/esm/src/proteingym/models/esm/__main__.py
+++ b/models/esm/src/proteingym/models/esm/__main__.py
@@ -2,11 +2,11 @@
 from typing import Annotated
 
 import typer
-from esm.model import infer, load
 from proteingym.base import Dataset
+from proteingym.base.model import ModelCard
 from rich.console import Console
 
-from proteingym.benchmark.model import ModelCard
+from .model import infer, load
 
 app = typer.Typer(
     help="ProteinGym2 - Model CLI",
diff --git a/models/esm/src/proteingym/models/esm/model.py b/models/esm/src/proteingym/models/esm/model.py
index 7860236b..d64ddbad 100644
--- a/models/esm/src/proteingym/models/esm/model.py
+++ b/models/esm/src/proteingym/models/esm/model.py
@@ -5,10 +5,9 @@
 from esm import pretrained
 from esm.data import Alphabet
 from proteingym.base import Dataset
+from proteingym.base.model import ModelCard
 from tqdm import tqdm
 
-from proteingym.benchmark.model import ModelCard
-
 from .preprocess import encode
 from .utils import compute_pppl, label_row
 
@@ -65,15 +64,24 @@ def infer(
     Raises:
         ValueError: If an unrecognized scoring strategy is specified
     """
-    assays = dataset.assays.meta.assays
-    targets = list(dataset.assays.meta.assays.keys())
+    assays = dataset.assays[0]
 
-    sequence = assays[targets[0]].constants["sequence"]
-    mutation_col = assays[targets[0]].constants["mutation_col"]
+    df = pd.DataFrame(
+        {
+            "mutation_col": [str(seq.value) for seq, _ in assays.records],
+            "target": [target["target"] for _, target in assays.records],
+        }
+    )
 
-    df = dataset.assays.data_frame
+    # For ESM zero-shot model, the schema is defined as ["mutation_col", "target"]
+    # with a reference sequence.
+    # For example: ["A2C", "-0.03"] with a reference sequence "AABB" refers to:
+    # in position 2, "A" is mutated to "C", which ends as "ACBB".
+    # But this reference sequence cannot be represented in the current proteingym-base dataset.
+    # As a workaround, variables are used to store this constant reference sequence.
+    reference_sequence = assays.variables["R"]
 
-    batch_tokens = encode(sequence, alphabet)
+    batch_tokens = encode(reference_sequence, alphabet)
 
     match model_card.hyper_params["scoring_strategy"]:
         case "wt-marginals":
@@ -82,8 +90,8 @@ def infer(
 
             df["pred"] = df.apply(
                 lambda row: label_row(
-                    row[mutation_col],
-                    sequence,
+                    row["mutation_col"],
+                    reference_sequence,
                     token_probs,
                     alphabet,
                     model_card.hyper_params["offset_idx"],
@@ -109,8 +117,8 @@ def infer(
 
             df["pred"] = df.apply(
                 lambda row: label_row(
-                    row[mutation_col],
-                    sequence,
+                    row["mutation_col"],
+                    reference_sequence,
                     token_probs,
                     alphabet,
                     model_card.hyper_params["offset_idx"],
@@ -123,8 +131,8 @@ def infer(
 
             df["pred"] = df.progress_apply(
                 lambda row: compute_pppl(
-                    row[mutation_col],
-                    sequence,
+                    row["mutation_col"],
+                    reference_sequence,
                     model,
                     alphabet,
                     model_card.hyper_params["offset_idx"],
@@ -137,6 +145,6 @@ def infer(
                 f"Unrecognized scoring strategy: {model_card.hyper_params['scoring_strategy']}"
             )
 
-    df.rename(columns={targets[0]: "test"}, inplace=True)
+    df.rename(columns={"target": "test"}, inplace=True)
 
     return df
diff --git a/models/esm/uv.lock b/models/esm/uv.lock
index d78af49c..e2b7e32c 100644
--- a/models/esm/uv.lock
+++ b/models/esm/uv.lock
@@ -6,134 +6,6 @@ resolution-markers = [
     "python_full_version < '3.13'",
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diff --git a/models/pls/Dockerfile b/models/pls/Dockerfile
index afb70c70..02c41dfc 100644
--- a/models/pls/Dockerfile
+++ b/models/pls/Dockerfile
@@ -11,8 +11,7 @@ COPY dist/proteingym*.whl dist/
 # Copy and install dependencies
 COPY README.md README.md
 COPY pyproject.toml pyproject.toml
-RUN uv sync --no-cache
-
 COPY src/ src/
+RUN uv sync --no-cache
 
 ENTRYPOINT ["uv", "run", "pls"]
diff --git a/models/pls/dist/.gitignore b/models/pls/dist/.gitignore
new file mode 100644
index 00000000..f59ec20a
--- /dev/null
+++ b/models/pls/dist/.gitignore
@@ -0,0 +1 @@
+*
\ No newline at end of file
diff --git a/models/pls/dist/proteingym_base-0.1.0b1-py3-none-any.whl b/models/pls/dist/proteingym_base-0.1.0b1-py3-none-any.whl
new file mode 100644
index 00000000..664b7237
Binary files /dev/null and b/models/pls/dist/proteingym_base-0.1.0b1-py3-none-any.whl differ
diff --git a/models/pls/pyproject.toml b/models/pls/pyproject.toml
index 97e24910..7ac08b1d 100644
--- a/models/pls/pyproject.toml
+++ b/models/pls/pyproject.toml
@@ -9,7 +9,6 @@ dependencies = [
     "numpy~=2.2.5",
     "scikit-learn~=1.7.0",
     "proteingym-base[biopython]",
-    "proteingym-benchmark",
     "polars[pyarrow]~=1.31.0",
 ]
 
@@ -21,12 +20,11 @@ requires = ["hatchling"]
 build-backend = "hatchling.build"
 
 [tool.uv.sources]
-# TODO: After proteingym-base and proteingym-benchmark are public repositories, below reference can be updated
+# TODO: After proteingym-base is public repositories, below reference can be updated
 proteingym-base = { path = "dist/proteingym_base-0.1.0b1-py3-none-any.whl" }
-proteingym-benchmark = { path = "dist/proteingym_benchmark-0.1.0b1-py3-none-any.whl" }
 
 [tool.hatch.build.targets.wheel]
-packages = ["src/"]
+packages = ["src/proteingym"]
 
 [tool.ruff]
 line-length = 88
diff --git a/models/pls/src/proteingym/models/pls/__main__.py b/models/pls/src/proteingym/models/pls/__main__.py
index 56dca018..84e380b4 100644
--- a/models/pls/src/proteingym/models/pls/__main__.py
+++ b/models/pls/src/proteingym/models/pls/__main__.py
@@ -3,10 +3,9 @@
 
 import typer
 from proteingym.base import Dataset
+from proteingym.base.model import ModelCard
 from rich.console import Console
 
-from proteingym.benchmark.model import ModelCard
-
 from .model import infer
 from .model import train as train_model
 
diff --git a/models/pls/src/proteingym/models/pls/model.py b/models/pls/src/proteingym/models/pls/model.py
index d7ca282e..a71285b7 100644
--- a/models/pls/src/proteingym/models/pls/model.py
+++ b/models/pls/src/proteingym/models/pls/model.py
@@ -2,10 +2,9 @@
 
 import polars as pl
 from proteingym.base import Dataset
+from proteingym.base.model import ModelCard
 from sklearn.cross_decomposition import PLSRegression
 
-from proteingym.benchmark.model import ModelCard
-
 from .preprocess import encode, load_x_and_y
 
 logger = logging.getLogger(__name__)
diff --git a/models/pls/src/proteingym/models/pls/preprocess.py b/models/pls/src/proteingym/models/pls/preprocess.py
index c783b755..dd5dbe8f 100644
--- a/models/pls/src/proteingym/models/pls/preprocess.py
+++ b/models/pls/src/proteingym/models/pls/preprocess.py
@@ -2,12 +2,12 @@
 from typing import Any
 
 import numpy as np
-from proteingym.base.dataset import Dataset
+from proteingym.base import Dataset
 
 logger = logging.getLogger(__name__)
 
 
-def load_x_and_y(dataset: Dataset, split) -> tuple[list[list[Any]], list[Any]]:
+def load_x_and_y(dataset: Dataset, split) -> tuple[list[Any], list[Any]]:
     """Load feature and target data from a dataset archive file for a specified split.
 
     This function applies the configured split strategy for the dataset,
@@ -19,8 +19,8 @@ def load_x_and_y(dataset: Dataset, split) -> tuple[list[list[Any]], list[Any]]:
         split: The data split to load (train, validation, or test).
 
     Returns:
-        tuple[list[list[Any]], list[Any]]: A tuple containing:
-            - split_X (list[list[Any]]): Feature data for the specified split, where each
+        tuple[list[Any], list[Any]]: A tuple containing:
+            - split_X (list[Any]): Feature data for the specified split, where each
                 inner list represents features for a single sample.
             - split_Y (list[Any]): Target values for the specified split.
 
@@ -30,26 +30,45 @@ def load_x_and_y(dataset: Dataset, split) -> tuple[list[list[Any]], list[Any]]:
         - Multiple targets and features support is planned for future implementation.
     """
 
-    targets = list(dataset.assays.meta.assays.keys())
-
     # TODO: Update split below
     # dataset.assays.add_split(
     #     split_strategy=SPLIT_STRATEGY_MAPPING[dataset.assays.meta.split_strategy](),
     #     targets=targets,
     # )
 
+    # TODO: Replace this dummy split with above split method
+    split_size = len(dataset.assays[0].records) // 3
+
     match split:
         case 1:
-            split_X = dataset.assays.train(targets=targets).x.iloc[:, 0].tolist()
-            split_Y = dataset.assays.train(targets=targets).y.iloc[:, 0].tolist()
+            split_X = [
+                str(seq.value) for seq, _ in dataset.assays[0].records[:split_size]
+            ]
+            split_Y = [
+                target["target"] for _, target in dataset.assays[0].records[:split_size]
+            ]
 
         case 2:
-            split_X = dataset.assays.valid(targets=targets).x.iloc[:, 0].tolist()
-            split_Y = dataset.assays.valid(targets=targets).y.iloc[:, 0].tolist()
+            split_X = [
+                str(seq.value)
+                for seq, _ in dataset.assays[0].records[split_size : split_size * 2]
+            ]
+            split_Y = [
+                target["target"]
+                for _, target in dataset.assays[0].records[split_size : split_size * 2]
+            ]
 
         case 3:
-            split_X = dataset.assays.test(targets=targets).x.iloc[:, 0].tolist()
-            split_Y = dataset.assays.test(targets=targets).y.iloc[:, 0].tolist()
+            split_X = [
+                str(seq.value)
+                for seq, _ in dataset.assays[0].records[split_size * 2 : split_size * 3]
+            ]
+            split_Y = [
+                target["target"]
+                for _, target in dataset.assays[0].records[
+                    split_size * 2 : split_size * 3
+                ]
+            ]
 
     logger.info("Loaded the dataset with splits X and Y.")
 
diff --git a/models/pls/uv.lock b/models/pls/uv.lock
index 7547f52f..5bfae994 100644
--- a/models/pls/uv.lock
+++ b/models/pls/uv.lock
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 name = "proteingym-base"
 version = "0.1.0b1"
@@ -1228,12 +207,13 @@ dependencies = [
     { name = "msgpack" },
     { name = "polars", extra = ["pyarrow"] },
     { name = "pydantic" },
+    { name = "python-frontmatter" },
     { name = "semver" },
     { name = "toml" },
     { name = "typer" },
 ]
 wheels = [
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 ]
 
 [package.metadata]
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     { name = "polars", extras = ["pyarrow"], specifier = ">=1.30.0,<2.0.0" },
     { name = "pydantic", specifier = ">=2.11.4,<3.0.0" },
+    { name = "python-frontmatter", specifier = ">=1.1.0" },
     { name = "semver", specifier = ">=3.0.4,<4.0.0" },
     { name = "toml", specifier = ">=0.10.2,<1.0.0" },
     { name = "typer", specifier = ">=0.16.0,<1.0.0" },
 ]
 
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-dependencies = [
-    { name = "boto3" },
-    { name = "dvc" },
-    { name = "proteingym-base" },
-    { name = "pycm" },
-    { name = "python-frontmatter" },
-    { name = "scipy" },
-    { name = "typer" },
-]
-wheels = [
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diff --git a/pyproject.toml b/pyproject.toml
index 0df33623..78ace764 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -13,6 +13,7 @@ dynamic = ["version"]  # Dynamically set hatch version using git tags
 requires-python = ">=3.12"
 dependencies = [
     "typer>=0.15.2",
+    "proteingym-base",
     "pycm>=4.3",
     "scipy>=1.15.3",
     "dvc>=3.59.2",
@@ -33,6 +34,10 @@ path = "src/proteingym/benchmark/__about__.py"
 [tool.hatch.build.targets.wheel]
 packages = ["src/proteingym"]
 
+[tool.uv.sources]
+# TODO: After proteingym-base is public repositories, below reference can be updated
+proteingym-base = { path = "dist/proteingym_base-0.1.0b1-py3-none-any.whl" }
+
 [tool.ruff]
 line-length = 88
 
diff --git a/uv.lock b/uv.lock
index 8607b5fd..fdd28c13 100644
--- a/uv.lock
+++ b/uv.lock
@@ -1,10 +1,6 @@
 version = 1
 revision = 3
 requires-python = ">=3.12"
-resolution-markers = [
-    "python_full_version >= '3.13'",
-    "python_full_version < '3.13'",
-]
 
 [[package]]
 name = "aiohappyeyeballs"
@@ -17,7 +13,7 @@ wheels = [
 
 [[package]]
 name = "aiohttp"
-version = "3.11.18"
+version = "3.13.0"
 source = { registry = "https://pypi.org/simple" }
 dependencies = [
     { name = "aiohappyeyeballs" },
@@ -28,40 +24,76 @@ dependencies = [
     { name = "propcache" },
     { name = "yarl" },
 ]
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