diff --git a/autointent/_optimization_config.py b/autointent/_optimization_config.py
index 6c55ee148..b314aa4bf 100644
--- a/autointent/_optimization_config.py
+++ b/autointent/_optimization_config.py
@@ -2,7 +2,7 @@
 
 from pydantic import BaseModel, PositiveInt
 
-from .configs import CrossEncoderConfig, DataConfig, EmbedderConfig, LoggingConfig
+from .configs import CrossEncoderConfig, DataConfig, EmbedderConfig, HFModelConfig, LoggingConfig
 from .custom_types import SamplerType
 
 
@@ -25,6 +25,8 @@ class OptimizationConfig(BaseModel):
 
     cross_encoder_config: CrossEncoderConfig = CrossEncoderConfig()
 
+    transformer_config: HFModelConfig = HFModelConfig()
+
     sampler: SamplerType = "brute"
     """See tutorial on optuna and presets."""
 
diff --git a/autointent/_pipeline/_pipeline.py b/autointent/_pipeline/_pipeline.py
index a141352ba..8966a4fbc 100644
--- a/autointent/_pipeline/_pipeline.py
+++ b/autointent/_pipeline/_pipeline.py
@@ -14,6 +14,7 @@
     CrossEncoderConfig,
     DataConfig,
     EmbedderConfig,
+    HFModelConfig,
     InferenceNodeConfig,
     LoggingConfig,
 )
@@ -67,10 +68,13 @@ def __init__(
             self.embedder_config = EmbedderConfig()
             self.cross_encoder_config = CrossEncoderConfig()
             self.data_config = DataConfig()
+            self.transformer_config = HFModelConfig()
         elif not isinstance(nodes[0], InferenceNode):
             assert_never(nodes)
 
-    def set_config(self, config: LoggingConfig | EmbedderConfig | CrossEncoderConfig | DataConfig) -> None:
+    def set_config(
+        self, config: LoggingConfig | EmbedderConfig | CrossEncoderConfig | DataConfig | HFModelConfig
+    ) -> None:
         """Set the configuration for the pipeline.
 
         Args:
@@ -84,6 +88,8 @@ def set_config(self, config: LoggingConfig | EmbedderConfig | CrossEncoderConfig
             self.cross_encoder_config = config
         elif isinstance(config, DataConfig):
             self.data_config = config
+        elif isinstance(config, HFModelConfig):
+            self.transformer_config = config
         else:
             assert_never(config)
 
@@ -133,6 +139,7 @@ def from_optimization_config(cls, config: dict[str, Any] | Path | str | Optimiza
         pipeline.set_config(optimization_config.data_config)
         pipeline.set_config(optimization_config.embedder_config)
         pipeline.set_config(optimization_config.cross_encoder_config)
+        pipeline.set_config(optimization_config.transformer_config)
         return pipeline
 
     def _fit(self, context: Context, sampler: SamplerType) -> None:
@@ -198,6 +205,7 @@ def fit(
         context.configure_logging(self.logging_config)
         context.configure_transformer(self.embedder_config)
         context.configure_transformer(self.cross_encoder_config)
+        context.configure_transformer(self.transformer_config)
 
         self.validate_modules(dataset, mode=incompatible_search_space)
 
diff --git a/autointent/modules/scoring/_ptuning/ptuning.py b/autointent/modules/scoring/_ptuning/ptuning.py
index 417cb138f..c0733134a 100644
--- a/autointent/modules/scoring/_ptuning/ptuning.py
+++ b/autointent/modules/scoring/_ptuning/ptuning.py
@@ -1,9 +1,10 @@
 """PTuningScorer class for ptuning-based classification."""
 
 from pathlib import Path
-from typing import Any
+from typing import Any, Literal
 
-from peft import PromptEncoderConfig, get_peft_model
+from peft import PromptEncoderConfig, PromptEncoderReparameterizationType, TaskType, get_peft_model
+from pydantic import PositiveInt
 
 from autointent import Context
 from autointent._callbacks import REPORTERS_NAMES
@@ -53,14 +54,19 @@ class PTuningScorer(BertScorer):
 
     name = "ptuning"
 
-    def __init__(
+    def __init__(  # noqa: PLR0913
         self,
         classification_model_config: HFModelConfig | str | dict[str, Any] | None = None,
-        num_train_epochs: int = 3,
-        batch_size: int = 8,
+        num_train_epochs: PositiveInt = 3,
+        batch_size: PositiveInt = 8,
         learning_rate: float = 5e-5,
         seed: int = 0,
         report_to: REPORTERS_NAMES | None = None,  # type: ignore[valid-type]
+        encoder_reparameterization_type: Literal["MLP", "LSTM"] = "LSTM",
+        num_virtual_tokens: PositiveInt = 10,
+        encoder_dropout: float = 0.1,
+        encoder_hidden_size: PositiveInt = 128,
+        encoder_num_layers: PositiveInt = 2,
         **ptuning_kwargs: Any,  # noqa: ANN401
     ) -> None:
         super().__init__(
@@ -71,17 +77,30 @@ def __init__(
             seed=seed,
             report_to=report_to,
         )
-        self._ptuning_config = PromptEncoderConfig(task_type="SEQ_CLS", **ptuning_kwargs)
+        self._ptuning_config = PromptEncoderConfig(
+            task_type=TaskType.SEQ_CLS,
+            encoder_reparameterization_type=PromptEncoderReparameterizationType(encoder_reparameterization_type),
+            num_virtual_tokens=num_virtual_tokens,
+            encoder_dropout=encoder_dropout,
+            encoder_hidden_size=encoder_hidden_size,
+            encoder_num_layers=encoder_num_layers,
+            **ptuning_kwargs,
+        )
 
     @classmethod
-    def from_context(
+    def from_context(  # noqa: PLR0913
         cls,
         context: Context,
         classification_model_config: HFModelConfig | str | dict[str, Any] | None = None,
-        num_train_epochs: int = 3,
-        batch_size: int = 8,
+        num_train_epochs: PositiveInt = 3,
+        batch_size: PositiveInt = 8,
         learning_rate: float = 5e-5,
         seed: int = 0,
+        encoder_reparameterization_type: Literal["MLP", "LSTM"] = "LSTM",
+        num_virtual_tokens: PositiveInt = 10,
+        encoder_dropout: float = 0.1,
+        encoder_hidden_size: PositiveInt = 128,
+        encoder_num_layers: PositiveInt = 2,
         **ptuning_kwargs: Any,  # noqa: ANN401
     ) -> "PTuningScorer":
         """Create a PTuningScorer instance using a Context object.
@@ -93,6 +112,11 @@ def from_context(
             batch_size: Batch size for training
             learning_rate: Learning rate for training
             seed: Random seed for reproducibility
+            encoder_reparameterization_type: Reparametrization type for the prompt encoder
+            num_virtual_tokens: Number of virtual tokens for the prompt encoder
+            encoder_dropout: Dropout for the prompt encoder
+            encoder_hidden_size: Hidden size for the prompt encoder
+            encoder_num_layers: Number of layers for the prompt encoder
             **ptuning_kwargs: Arguments for PromptEncoderConfig
         """
         if classification_model_config is None:
@@ -107,6 +131,11 @@ def from_context(
             learning_rate=learning_rate,
             seed=seed,
             report_to=report_to,
+            encoder_reparameterization_type=encoder_reparameterization_type,
+            num_virtual_tokens=num_virtual_tokens,
+            encoder_dropout=encoder_dropout,
+            encoder_hidden_size=encoder_hidden_size,
+            encoder_num_layers=encoder_num_layers,
             **ptuning_kwargs,
         )
 
diff --git a/docs/optimizer_config.schema.json b/docs/optimizer_config.schema.json
index 27e83abe8..f9e9f7e18 100644
--- a/docs/optimizer_config.schema.json
+++ b/docs/optimizer_config.schema.json
@@ -253,6 +253,48 @@
             "title": "EmbedderConfig",
             "type": "object"
         },
+        "HFModelConfig": {
+            "additionalProperties": false,
+            "properties": {
+                "model_name": {
+                    "default": "prajjwal1/bert-tiny",
+                    "description": "Name of the hugging face repository with transformer model.",
+                    "title": "Model Name",
+                    "type": "string"
+                },
+                "batch_size": {
+                    "default": 32,
+                    "description": "Batch size for model inference.",
+                    "exclusiveMinimum": 0,
+                    "title": "Batch Size",
+                    "type": "integer"
+                },
+                "device": {
+                    "anyOf": [
+                        {
+                            "type": "string"
+                        },
+                        {
+                            "type": "null"
+                        }
+                    ],
+                    "default": null,
+                    "description": "Torch notation for CPU or CUDA.",
+                    "title": "Device"
+                },
+                "tokenizer_config": {
+                    "$ref": "#/$defs/TokenizerConfig"
+                },
+                "trust_remote_code": {
+                    "default": false,
+                    "description": "Whether to trust the remote code when loading the model.",
+                    "title": "Trust Remote Code",
+                    "type": "boolean"
+                }
+            },
+            "title": "HFModelConfig",
+            "type": "object"
+        },
         "LoggingConfig": {
             "additionalProperties": false,
             "description": "Configuration for the logging.",
@@ -442,6 +484,20 @@
                 "train_head": false
             }
         },
+        "transformer_config": {
+            "$ref": "#/$defs/HFModelConfig",
+            "default": {
+                "model_name": "prajjwal1/bert-tiny",
+                "batch_size": 32,
+                "device": null,
+                "tokenizer_config": {
+                    "max_length": null,
+                    "padding": true,
+                    "truncation": true
+                },
+                "trust_remote_code": false
+            }
+        },
         "sampler": {
             "default": "brute",
             "enum": [