Pad and mask the sequences in each batch

src/hyperparameters.py

@@ -11,6 +11,7 @@ class Hyperparameters:
         learning_rate=0.004,
         l2_rate=0.001,
         log_directory="logs",
+        max_length=80,
     ):
         self.data_file = data_file
         self.label_file = label_file
@@ -22,3 +23,4 @@ class Hyperparameters:
         self.learning_rate = learning_rate
         self.l2_rate = l2_rate
         self.log_directory = log_directory
+        self.max_length = max_length

src/model.py

@@ -17,7 +17,8 @@ def build_model(hyperparams) -> Model:
     """
     model = Sequential(
         [
-            Input(shape=(None, len(BASES))),
+            Input(shape=(None, hyperparams.max_length, len(BASES))),
+            Masking(mask_value=-1),
             Conv1D(
                 filters=16,
                 kernel_size=5,

src/preprocessing.py

@@ -115,8 +115,13 @@ def read_dataset(filepath, hyperparams) -> TFRecordDataset:
     data_input = TFRecordDataset(filenames=filepath)
     dataset = data_input.map(map_func=process_input, num_parallel_calls=AUTOTUNE)
     shuffled_dataset = dataset.shuffle(buffer_size=10000, seed=42)
-    batched_dataset = shuffled_dataset.batch(batch_size=hyperparams.batch_size).repeat(
+    batched_dataset = shuffled_dataset.padded_batch(
-        count=hyperparams.epochs
+        batch_size=hyperparams.batch_size,
+        padded_shapes=(
+            [hyperparams.max_length, len(BASES)],
+            [hyperparams.max_length, len(BASES)],
+        ),
+        padding_values=-1.0,
     )
     return batched_dataset