diff --git a/doc/self-contrast.md b/doc/self-contrast.md
new file mode 100644
index 0000000..80a2acc
--- /dev/null
+++ b/doc/self-contrast.md
@@ -0,0 +1,174 @@
+# Self-Contrast: Analysis
+
+## What Is Self-Contrast?
+
+Self-contrast is a data-level strategy for handling rows in the pre-training dataset
+that have **no code transformation** (i.e., `transformed` is `None`).
+Instead of discarding these rows, self-contrast copies the original code into the
+`transformed` field, creating a pair where both the anchor and the augmentation are
+the **same source code**.
+
+Because MLM masking is applied **independently** to each copy
+(`DataCollatorForLanguageModeling` with `mlm_probability=0.15`), the model sees
+two views of the same code with **different random masks**. This produces an "easy"
+contrastive pair — same semantics, same syntax, different masked tokens.
+
+### Implementation
+
+The entire mechanism is a single `dataset.map` call in `pretrain.py:268-276`:
+
+```python
+if self_contrast:
+    dataset = dataset.map(
+        lambda transformed, code: {
+            "transformed": transformed if transformed is not None else code
+        },
+        input_columns=["transformed", "code"],
+        num_proc=num_proc,
+    )
+```
+
+No changes are needed in the loss functions, model architecture, or training loop.
+The contrastive loss (InfoNCE, SupCon, or Grouped) treats self-contrast pairs
+identically to invariant-contrast pairs.
+
+## Why It Is Feasible
+
+### 1. MLM Masking Creates Distinct Views
+
+Even though both copies share the same token sequence, the `DataCollatorForLanguageModeling`
+samples a fresh 15% mask for each copy independently. This means:
+
+- The `code_input_ids` has some tokens replaced with `[MASK]`.
+- The `aug_input_ids` has a **different** set of tokens replaced with `[MASK]`.
+
+The CLS embeddings produced by the encoder therefore differ, because the model
+conditions on different visible tokens. This difference is what makes the contrastive
+signal non-trivial — the model must learn that both masked views correspond to the
+same underlying program.
+
+### 2. Stochastic Masking as a Natural Data Augmentation
+
+MLM masking is itself a form of stochastic data augmentation.
+Given a sequence of length $L$, the number of possible 15%-masks is
+$\binom{L}{\lfloor 0.15L \rfloor}$, which is astronomically large for typical code
+sequences ($L \approx 100$–$256$). Each training step therefore produces a genuinely
+novel pair, even if the underlying code is the same. The model never sees the exact
+same (mask_a, mask_b) combination twice in practice.
+
+### 3. Zero Implementation Overhead
+
+Self-contrast requires no additional model components, no separate training stage,
+and no architectural changes. It is purely a data-filling operation that replaces
+`None` with the original code string. The downstream data collator, tokenizer,
+and loss functions are completely agnostic to whether a pair is self-contrast or
+invariant-contrast.
+
+### 4. Consistency with the Shared-Encoder Design
+
+InvPT uses a **single shared encoder** for both the original and transformed code
+(unlike ContraBERT's momentum contrast with a separate momentum encoder).
+In this architecture, the same parameters process both copies.
+Self-contrast is a natural fit: since the encoder is shared, feeding the same code
+twice with different masks is equivalent to asking "do two partial observations of
+the same program yield similar representations?" — a well-defined learning objective.
+
+## Why It Is Beneficial
+
+### 1. Implicit Curriculum Learning
+
+Self-contrast creates an implicit curriculum with two difficulty levels:
+
+| Pair Type          | Difficulty | Source of Difference                           |
+| ------------------ | ---------- | ---------------------------------------------- |
+| Self-contrast      | Easy       | Different MLM masks only                       |
+| Invariant-contrast | Hard       | Syntactic transformation + different MLM masks |
+
+**Easy pairs** (self-contrast) produce CLS embeddings that are already relatively
+close, generating small but consistent gradients that stabilize training.
+**Hard pairs** (invariant-contrast) produce more distant embeddings, generating
+larger gradients that push the model to learn semantic invariance.
+
+Training on both simultaneously provides the benefits of curriculum learning
+without explicit scheduling: the easy pairs act as a regularizer, preventing the
+model from being destabilized by the harder invariant pairs early in training.
+As the model improves, self-contrast pairs become trivially easy and the learning
+signal shifts toward the harder invariant pairs, naturally concentrating the
+gradient on the most informative examples.
+
+### 2. Data Efficiency — No Wasted Rows
+
+Not every code sample in the dataset has a successful transformation.
+Transformation operators may fail (e.g., no for-loops to convert, no local
+variables to rename). Without self-contrast, these rows are **discarded**:
+
+```python
+# Without self-contrast: rows without augmentation are dropped
+dataset = dataset.filter(
+    lambda transformed: transformed is not None and transformed != "",
+    input_columns=["transformed"],
+)
+```
+
+This wastes a potentially large fraction of the dataset. With self-contrast,
+**every row contributes** to both the MLM and contrastive objectives. The model
+sees more code, learns better MLM representations, and the contrastive batch
+is denser (more positives in SupCon mode, since rows sharing the same
+`function_id` all participate).
+
+### 3. MLM Regularization on the Full Corpus
+
+Even if the contrastive gradient from a self-contrast pair is small, the **MLM
+loss** on that pair is still fully informative — the model must predict different
+masked tokens in each copy. Retaining these rows ensures the MLM objective
+covers the entire pre-training corpus, not just the transformable subset.
+This is important because the transformation operators have language-specific
+coverage (e.g., Python lacks `F2W` and `W2F`), so dropping untransformable rows
+would bias the MLM objective toward code containing certain syntactic patterns.
+
+### 4. Representation Stability via Alignment
+
+Self-contrast directly optimizes what Chen & He (2021) call the **alignment**
+property of contrastive representations: embeddings of the same instance
+(under different views) should be close. By ensuring the encoder maps different
+masked views of the same code to similar CLS vectors, self-contrast encourages
+a smooth, stable representation manifold where small input perturbations
+(missing tokens) do not cause large embedding shifts. This stability transfers
+to downstream tasks where inputs may be noisy or partial.
+
+### 5. Compatibility with SupCon Multi-Positive Masking
+
+In SupCon mode, all embeddings sharing the same `function_id` are treated as
+positives. Self-contrast rows share `function_id` with their corresponding
+invariant-contrast rows (since `function_id` is a hash of the original code).
+This means self-contrast rows add **additional positive pairs** to the SupCon
+loss, increasing the effective number of positives per anchor. Khosla et al.
+(2020) showed that SupCon benefits from more positives per class, making
+self-contrast especially synergistic with the SupCon contrastive mode.
+
+## Connection to Prior Work
+
+Self-contrast is conceptually related to several established techniques:
+
+- **SimCLR** (Chen et al., 2020): Uses two random augmentations of the same
+  image as a positive pair. Self-contrast uses two random MLM masks of the
+  same code as a positive pair — the MLM mask plays the role of the
+  stochastic augmentation.
+- **Dropout-as-augmentation** (Gao et al., 2021, SimCSE): Passes the same
+  sentence through the encoder twice with different dropout masks to create
+  positive pairs. Self-contrast is analogous but uses MLM masking instead
+  of dropout as the source of stochasticity.
+- **BERT's own MLM objective**: Standard MLM already trains the model to be
+  robust to random token masking. Self-contrast extends this to the
+  contrastive objective, requiring not just correct token prediction but
+  also consistent sequence-level (CLS) representations across masks.
+
+## Summary
+
+Self-contrast is a simple, zero-cost data strategy that:
+
+1. Turns untransformable rows into useful training signal (data efficiency).
+2. Creates an implicit easy/hard curriculum (training stability).
+3. Ensures MLM coverage of the full corpus (unbiased language modeling).
+4. Encourages alignment and smoothness in the representation space (downstream robustness).
+5. Requires no changes to the model, loss, or training loop (implementation simplicity).
diff --git a/experiments/grouped/codebert.yaml b/experiments/grouped/codebert.yaml
index b414305..a1ea518 100644
--- a/experiments/grouped/codebert.yaml
+++ b/experiments/grouped/codebert.yaml
@@ -2,7 +2,7 @@
 # Effective batch size: 16 * 16 = 256
 # Usage: python modeling/cli.py run experiments/grouped/codebert.yaml
 
-dataset_path: "data/aug_csn.jsonl"
+dataset_path: "data/csn.jsonl"
 model_name: "microsoft/codebert-base"
 
 batch_size: 32
@@ -19,3 +19,4 @@ max_seq_length: 512
 
 contra_mode: "grouped"
 max_num_augs: 6
+self_contrast: true
diff --git a/experiments/grouped/contrabert_c.yaml b/experiments/grouped/contrabert_c.yaml
index a7456e4..7d4b740 100644
--- a/experiments/grouped/contrabert_c.yaml
+++ b/experiments/grouped/contrabert_c.yaml
@@ -2,7 +2,7 @@
 # Effective batch size: 16 * 16 = 256
 # Usage: python modeling/cli.py run experiments/grouped/contrabert_c.yaml
 
-dataset_path: "data/aug_csn.jsonl"
+dataset_path: "data/csn.jsonl"
 model_name: "./saved_models/ContraBERT_C"
 tokenizer_name: "microsoft/codebert-base"
 
@@ -20,3 +20,4 @@ max_seq_length: 512
 
 contra_mode: "grouped"
 max_num_augs: 6
+self_contrast: true
diff --git a/experiments/grouped/contrabert_g.yaml b/experiments/grouped/contrabert_g.yaml
index d9ae460..1c7cfd1 100644
--- a/experiments/grouped/contrabert_g.yaml
+++ b/experiments/grouped/contrabert_g.yaml
@@ -2,7 +2,7 @@
 # Effective batch size: 16 * 16 = 256
 # Usage: python modeling/cli.py run experiments/grouped/contrabert_g.yaml
 
-dataset_path: "data/aug_csn.jsonl"
+dataset_path: "data/csn.jsonl"
 model_name: "./saved_models/ContraBERT_G"
 tokenizer_name: "microsoft/graphcodebert-base"
 
@@ -20,3 +20,4 @@ max_seq_length: 512
 
 contra_mode: "grouped"
 max_num_augs: 6
+self_contrast: true
diff --git a/experiments/grouped/graphcodebert.yaml b/experiments/grouped/graphcodebert.yaml
index da9ff73..d7eb62a 100644
--- a/experiments/grouped/graphcodebert.yaml
+++ b/experiments/grouped/graphcodebert.yaml
@@ -2,7 +2,7 @@
 # Effective batch size: 16 * 16 = 256
 # Usage: python modeling/cli.py run experiments/grouped/graphcodebert.yaml
 
-dataset_path: "data/aug_csn.jsonl"
+dataset_path: "data/csn.jsonl"
 model_name: "microsoft/graphcodebert-base"
 
 batch_size: 32
@@ -19,3 +19,4 @@ max_seq_length: 512
 
 contra_mode: "grouped"
 max_num_augs: 6
+self_contrast: true
diff --git a/experiments/supcon/codebert.yaml b/experiments/supcon/codebert.yaml
index fb70d1a..8dca2c0 100644
--- a/experiments/supcon/codebert.yaml
+++ b/experiments/supcon/codebert.yaml
@@ -2,7 +2,7 @@
 # Effective batch size: 64 * 4 = 256
 # Usage: python modeling/cli.py run experiments/supcon/codebert.yaml
 
-dataset_path: "data/aug_csn.jsonl"
+dataset_path: "data/csn.jsonl"
 model_name: "microsoft/codebert-base"
 
 batch_size: 256
@@ -18,3 +18,4 @@ temperature: 0.1
 max_seq_length: 512
 
 contra_mode: "supcon"
+self_contrast: true
diff --git a/experiments/supcon/contrabert_c.yaml b/experiments/supcon/contrabert_c.yaml
index 039e83f..14d4c56 100644
--- a/experiments/supcon/contrabert_c.yaml
+++ b/experiments/supcon/contrabert_c.yaml
@@ -2,7 +2,7 @@
 # Effective batch size: 64 * 4 = 256
 # Usage: python modeling/cli.py run experiments/supcon/contrabert_c.yaml
 
-dataset_path: "data/aug_csn.jsonl"
+dataset_path: "data/csn.jsonl"
 model_name: "./saved_models/ContraBERT_C"
 tokenizer_name: "microsoft/codebert-base"
 
@@ -19,3 +19,4 @@ temperature: 0.1
 max_seq_length: 512
 
 contra_mode: "supcon"
+self_contrast: true
diff --git a/experiments/supcon/contrabert_g.yaml b/experiments/supcon/contrabert_g.yaml
index eb262b6..f3fe39a 100644
--- a/experiments/supcon/contrabert_g.yaml
+++ b/experiments/supcon/contrabert_g.yaml
@@ -2,7 +2,7 @@
 # Effective batch size: 64 * 4 = 256
 # Usage: python modeling/cli.py run experiments/supcon/contrabert_g.yaml
 
-dataset_path: "data/aug_csn.jsonl"
+dataset_path: "data/csn.jsonl"
 model_name: "./saved_models/ContraBERT_G"
 tokenizer_name: "microsoft/graphcodebert-base"
 
@@ -19,3 +19,4 @@ temperature: 0.1
 max_seq_length: 512
 
 contra_mode: "supcon"
+self_contrast: true
diff --git a/experiments/supcon/graphcodebert.yaml b/experiments/supcon/graphcodebert.yaml
index 8d8c835..e5fc701 100644
--- a/experiments/supcon/graphcodebert.yaml
+++ b/experiments/supcon/graphcodebert.yaml
@@ -2,7 +2,7 @@
 # Effective batch size: 64 * 4 = 256
 # Usage: python modeling/cli.py run experiments/supcon/graphcodebert.yaml
 
-dataset_path: "data/aug_csn.jsonl"
+dataset_path: "data/csn.jsonl"
 model_name: "microsoft/graphcodebert-base"
 
 batch_size: 256 # 64
@@ -18,3 +18,4 @@ temperature: 0.1
 max_seq_length: 512
 
 contra_mode: "supcon"
+self_contrast: true
diff --git a/modeling/cli.py b/modeling/cli.py
index 28cef55..97c548a 100644
--- a/modeling/cli.py
+++ b/modeling/cli.py
@@ -24,18 +24,26 @@ def run(
         Optional[float],
         typer.Option("--sample-rate", "-sr", help="Override sample rate from config."),
     ] = None,
+    self_contrast: Annotated[
+        Optional[bool],
+        typer.Option(
+            help="Override self-contrast setting from config. Use --no-self-contrast to disable.",
+        ),
+    ] = None,
 ) -> None:
     """Run pre-training from a YAML config file.
 
     All parameters are read from the config file to ensure full reproducibility.
-    Use --sample-rate to override the dataset sampling fraction.
+    Use --sample-rate / --no-self-contrast to override specific settings.
 
-    Example: python -m modeling run experiments/base.yaml --sample-rate 0.1
+    Example: python -m modeling run experiments/base.yaml --no-self-contrast
     """
     cfg = load_config(config)
     kwargs = asdict(cfg)
     if sample_rate is not None:
         kwargs["sample_rate"] = sample_rate
+    if self_contrast is not None:
+        kwargs["self_contrast"] = self_contrast
     main(**kwargs)
 
 
@@ -88,6 +96,12 @@ def pretrain(
     max_num_augs: Annotated[
         int, typer.Option(help="Max augmentations per anchor (grouped mode).")
     ] = 6,
+    self_contrast: Annotated[
+        bool,
+        typer.Option(
+            help="Use self-contrast (same code, different MLM masks) for rows without augmentation. If disabled, rows without augmentation are dropped."
+        ),
+    ] = True,
 ) -> None:
     """Run pre-training with all parameters specified as CLI options.
 
@@ -113,6 +127,7 @@ def pretrain(
         checkpoint=checkpoint,
         contra_mode=contra_mode,
         max_num_augs=max_num_augs,
+        self_contrast=self_contrast,
     )
 
 
diff --git a/modeling/config.py b/modeling/config.py
index 4771ea2..f24b365 100644
--- a/modeling/config.py
+++ b/modeling/config.py
@@ -32,6 +32,7 @@ class PretrainConfig:
     tokenizer_name: str | None = None
     contra_mode: ContraMode = ContraMode.INFO_NCE
     max_num_augs: int = 6
+    self_contrast: bool = True
 
 
 def load_config(path: str | Path) -> PretrainConfig:
diff --git a/modeling/pretrain.py b/modeling/pretrain.py
index fa92802..38ee846 100644
--- a/modeling/pretrain.py
+++ b/modeling/pretrain.py
@@ -223,6 +223,7 @@ def main(
     tokenizer_name: str | None = None,
     contra_mode: ContraMode = "info_nce",
     max_num_augs: int = 6,
+    self_contrast: bool = True,
 ):
     set_seed(seed)
 
@@ -264,11 +265,23 @@ def main(
         }
     )
     dataset = load_dataset("json", data_files=dataset_path, features=features)["train"]
-    dataset = dataset.filter(
-        lambda transformed: transformed is not None,
-        input_columns=["transformed"],
-        num_proc=num_proc,
-    )
+    if self_contrast:
+        # For rows without a transformation, use the original code as the
+        # augmentation (self-contrast: same code, different MLM masks).
+        dataset = dataset.map(
+            lambda transformed, code: {
+                "transformed": transformed if transformed is not None else code
+            },
+            input_columns=["transformed", "code"],
+            num_proc=num_proc,
+        )
+    else:
+        # Drop rows that have no real augmentation.
+        dataset = dataset.filter(
+            lambda transformed: transformed is not None and transformed != "",
+            input_columns=["transformed"],
+            num_proc=num_proc,
+        )
 
     if sample_rate < 1.0:
         dataset = dataset.shuffle(seed=seed).select(