Trainer .evaluate() method returns one less prediction, but training runs fine (GPT-2 fine-tuning)
I’ve been breaking my head about this bug in my code for two days now. I have a set of german texts that I want to classify into one of 10 classes. The training runs smoothly, I have problems with the evaluation. Obviously I don’t share the whole texts, let me know if that is required, but they are confidential, so I’d have to make a mock example.Here is the code I use to get my data:train_texts, val_texts, train_labels, val_labels = train_test_split(texts, labels, random_state=111, test_size=0.1)

print("TRAIN TEXTS LENGTH", len(train_texts))
print("VAL TEXTS LENGTH", len(val_texts))
print("TRAIN LABELS LENGTH", len(train_labels))
print("VAL LABELS LENGTH", len(val_labels))TRAIN TEXTS LENGTH 36VAL TEXTS LENGTH 4TRAIN LABELS LENGTH 36VAL LABELS LENGTH 4Here is the code I have. First I prepare the model:###########################
# Prepare model
###########################

# Tokenizer 
tokenizer = AutoTokenizer.from_pretrained("benjamin/gerpt2", model_max_len = 300)
tokenizer.padding_side = "left" # GPT-2 must be padded to the left
tokenizer.pad_token = tokenizer.eos_token

# Model
config = GPT2Config.from_pretrained(pretrained_model_name_or_path="benjamin/gerpt2",
                                    id2label = id2label, #dictionary of {'id': 'label'}
                                    label2id = label2id) #dictionary of {'label': 'id'}

model = AutoModelForSequenceClassification.from_pretrained("benjamin/gerpt2", num_labels = 10)
model.resize_token_embeddings(len(tokenizer))
model.config.pad_token_id = model.config.eos_token_idThen I create dataset and tokenize text (see custom defined classes and function):def tokenize_text(text, tokenizer):
    '''
    Tokenizes text using a loaded tokenizer
    '''
    return tokenizer(text, max_length=300, truncation=True, padding=True)

class CustomDataset(torch.utils.data.Dataset):
    '''
    Defines a Dataset class to feed the model.
    '''
    def __init__(self, encodings, labels=None):
        
        '''
        Initializes the class with the preprocessed text (encodings), labels and number of examples.      
        '''
        
        self.encodings = encodings
        self.labels = labels
        self.n_examples = len(self.labels)

    def __getitem__(self, idx):
        
        '''
        Defines a method that pulls a single item with its idx from the dataset.
        '''
        
        item = {key: torch.tensor(val[idx]) for key, val in self.encodings.items()} # get from dictionary
        if self.labels:
          item["labels"] = torch.tensor(self.labels[idx])
        
        return item

    def __len__(self):
        '''
        Defines a method that returns the length of the dataset.
        '''
        return len(self.encodings["input_ids"])

###########################
# Encode text
###########################

train_encodings = tokenize_text(train_texts, tokenizer)
val_encodings = tokenize_text(val_texts, tokenizer)

###########################
# Create dataset objects
###########################

train_dataset = CustomDataset(train_encodings, train_labels)
val_dataset = CustomDataset(val_encodings, val_labels)Now I created my own Trainer class and compute metrics because I want to use theweightargument in my loss function that I defined:###########################
# Training arguments
###########################

def compute_metrics(pred):
    '''
    Calculates metrics to evaluate model.
    '''
    labels = pred.label_ids
    preds = pred.predictions.argmax(-1)
    
    print('\npred.predictions:\n', pred.predictions)
    print('\npred:\n', pred)
    print()
    print('y_true', labels)
    print('y_hat', preds)
   
    precision, recall, f1, _ = precision_recall_fscore_support(labels, preds, average='weighted')
    acc = accuracy_score(labels, preds)
    return {
        'accuracy': acc,
        'f1': f1,
        'precision': precision,
        'recall': recall
    }

# Model Artifacts should fall into this folder (or sub folders)
artifacts_out_dir = './outputs'

training_args = TrainingArguments(
    output_dir=artifacts_out_dir,
    # checkpoint saving strategy
    overwrite_output_dir=True,
    evaluation_strategy = 'epoch',
    # model hyperparameters
    num_train_epochs=1,
    per_device_train_batch_size=8,
    per_device_eval_batch_size=8,
    warmup_steps=10,
    weight_decay=0.01,
# evaluation strategy and logging
    logging_dir='./logs/tensorboard',
    logging_steps=2
)

class TrainerCustom(transformers.Trainer):

    def __init__(self, weights, *args, **kwargs):
        super().__init__(*args, **kwargs)

        # initialize weights from argument
        self.weights = weights

    def compute_loss(self, model, inputs, return_outputs=False):
        """
        How the loss is computed by Trainer. By default, all models return the loss in the first element.
        Subclass and override for custom behavior.
        """

        labels = inputs.pop("labels")

        outputs, _ = model(**inputs, return_dict=False) # returns tuple, that is why '_'

        # set to same device as labels
        self.weights = self.weights.to(labels.device)

        print("LABELS:", labels)
        print('LABELS device:', labels.device)
        print("WEIGHTS:", self.weights)
        print('WEIGHTS device:', self.weights.device)

        # Save past state if it exists
        if self.args.past_index >= 0:
            self._past = outputs[self.args.past_index]

        cross_entropy_loss_func = torch.nn.CrossEntropyLoss(weight = self.weights)
        
        print('OUTPUTS:', outputs)
        
        loss = cross_entropy_loss_func(outputs, labels.long()) # set labels to TensorLong, got error before

        print('LOSS', loss)

        return (loss, outputs) if return_outputs else lossNow I obviously run just debug mode (1 epoch, 36 train examples, 4 val examples).###########################
# Trainer class
###########################

trainer = TrainerCustom(
    model=model,
    args=training_args,
    compute_metrics=compute_metrics, #own defined function see above
    train_dataset=train_dataset,
    eval_dataset=val_dataset,
    weights = torch.tensor([1.2000, 0.9000, 1.2000, 0.9000, 0.9000, 0.9000, 0.9000, 1.8000, 0.9000, 0.9000]) # 10 weights for 10 classes
)Now I run training (evaluation happens as part of training due to arguments I set):print('\nRunning training...\n')
trainer.train()However, the issue is thatthe .evaluate() function for some reason returns correct number of labels. but one less than batch size predictions - hence my lengths don’t match and I get an error. See below. I print it all so I found where the bug is, I looked into the source code, but just can’t find where I’m making a mistake.# TRAINING STEP PRINTS - EVERYTHING IS OK
LABELS: tensor([3, 9, 5, 9, 0, 6, 4, 0], dtype=torch.int32)
LABELS device: cpu
WEIGHTS: tensor([1.2000, 0.9000, 1.2000, 0.9000, 0.9000, 0.9000, 0.9000, 1.8000, 0.9000,
        0.9000])
WEIGHTS device: cpu
OUTPUTS: tensor([[-0.0889,  0.2450,  0.3983,  0.1111, -0.1511, -0.0520, -0.3428,  0.2376,
         -0.1851, -0.5946],
        [ 0.3004,  0.1739,  0.4019,  0.1611, -0.2102, -0.1775, -0.0751,  0.4822,
         -0.3875, -0.5656],
        [ 0.2611,  0.1720,  0.0378,  0.0174, -0.1998, -0.1694,  0.0667,  0.7277,
         -0.0311, -0.4646],
        [ 0.3728,  0.6940,  0.0792,  0.1359, -0.0296,  0.2614, -0.1489,  0.5426,
         -0.0150, -0.7283],
        [ 0.3806,  0.3427,  0.2283, -0.0392, -0.0176, -0.2239, -0.1351,  0.8266,
         -0.4894, -0.5863],
        [ 0.0585,  0.3695,  0.5742, -0.7659, -0.1160, -0.2615,  0.1515,  1.7408,
         -0.7622, -1.0512],
        [-0.1374,  0.0696,  0.1904,  0.2616,  0.1822, -0.3327, -0.4270,  0.6404,
         -0.2022, -0.5745],
        [ 0.4530,  0.3680,  0.4304, -0.4875, -0.4661, -0.2198,  0.0557,  0.4714,
         -0.3884, -0.2292]], grad_fn=<IndexBackward>)
LOSS tensor(2.4015, grad_fn=<NllLossBackward>)# EVAL STEP 

LABELS: tensor([0, 2, 7, 7], dtype=torch.int32)
LABELS device: cpu
WEIGHTS: tensor([1.2000, 0.9000, 1.2000, 0.9000, 0.9000, 0.9000, 0.9000, 1.8000, 0.9000,
        0.9000])
WEIGHTS device: cpu
OUTPUTS: tensor([[ 0.1938, -0.2064,  0.3387,  0.0504,  0.0684, -0.2160, -0.2775,  0.4145,
         -0.2933, -0.1107],
        [ 0.1445,  0.0269,  0.1467,  0.1527, -0.2904,  0.0661, -0.2611,  0.5330,
         -0.0186, -0.4184],
        [-0.0918, -0.0234,  0.2311,  0.1614, -0.1304, -0.1700, -0.1917,  0.2001,
         -0.3553, -0.2138],
        [-0.0918, -0.0234,  0.2311,  0.1614, -0.1304, -0.1700, -0.1917,  0.2001,
         -0.3553, -0.2138]])
LOSS tensor(2.1039)

pred.predictions:
 [[ 0.14445858  0.02692143  0.14672504  0.1527456  -0.29039353  0.06611381
  -0.26105392  0.5329592  -0.01855119 -0.41837007]
 [-0.09184867 -0.02340093  0.23106857  0.16139469 -0.13035089 -0.17000316
  -0.19174051  0.20007178 -0.3553058  -0.2137518 ]
 [-0.09184867 -0.02340093  0.23106857  0.16139469 -0.13035089 -0.17000316
  -0.19174051  0.20007178 -0.3553058  -0.2137518 ]]

pred:
 EvalPrediction(predictions=array([[ 0.14445858,  0.02692143,  0.14672504,  0.1527456 , -0.29039353,
         0.06611381, -0.26105392,  0.5329592 , -0.01855119, -0.41837007],
       [-0.09184867, -0.02340093,  0.23106857,  0.16139469, -0.13035089,
        -0.17000316, -0.19174051,  0.20007178, -0.3553058 , -0.2137518 ],
       [-0.09184867, -0.02340093,  0.23106857,  0.16139469, -0.13035089,
        -0.17000316, -0.19174051,  0.20007178, -0.3553058 , -0.2137518 ]],
      dtype=float32), label_ids=array([0, 2, 7, 7]))

y_true [0 2 7 7] 
y_hat [7 2 2]As you can see, I get y_hatone less predicted class. Not sure why - the bug must be in the step above, as I only get three tensors instead of 4 of class probabilities (in the EvalPrediction obj).Here is the error message:---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
~\AppData\Local\Temp/ipykernel_8820/2277851298.py in <module>
      4 
      5 print('\nRunning training...\n')
----> 6 trainer.train()

~\Anaconda3\envs\mailbot\lib\site-packages\transformers\trainer.py in train(self, resume_from_checkpoint, trial, ignore_keys_for_eval, **kwargs)
   1405 
   1406             self.control = self.callback_handler.on_epoch_end(args, self.state, self.control)
-> 1407             self._maybe_log_save_evaluate(tr_loss, model, trial, epoch, ignore_keys_for_eval)
   1408 
   1409             if DebugOption.TPU_METRICS_DEBUG in self.args.debug:

~\Anaconda3\envs\mailbot\lib\site-packages\transformers\trainer.py in _maybe_log_save_evaluate(self, tr_loss, model, trial, epoch, ignore_keys_for_eval)
   1512         metrics = None
   1513         if self.control.should_evaluate:
-> 1514             metrics = self.evaluate(ignore_keys=ignore_keys_for_eval)
   1515             self._report_to_hp_search(trial, epoch, metrics)
   1516 

~\Anaconda3\envs\mailbot\lib\site-packages\transformers\trainer.py in evaluate(self, eval_dataset, ignore_keys, metric_key_prefix)
   2156             prediction_loss_only=True if self.compute_metrics is None else None,
   2157             ignore_keys=ignore_keys,
-> 2158             metric_key_prefix=metric_key_prefix,
   2159         )
   2160 

~\Anaconda3\envs\mailbot\lib\site-packages\transformers\trainer.py in evaluation_loop(self, dataloader, description, prediction_loss_only, ignore_keys, metric_key_prefix)
   2390         # Metrics!
   2391         if self.compute_metrics is not None and all_preds is not None and all_labels is not None:
-> 2392             metrics = self.compute_metrics(EvalPrediction(predictions=all_preds, label_ids=all_labels))
   2393         else:
   2394             metrics = {}

~\AppData\Local\Temp/ipykernel_8820/1156443582.py in compute_metrics(pred)
    120     print('y_hat', preds)
    121 
--> 122     precision, recall, f1, _ = precision_recall_fscore_support(labels, preds, average='weighted')
    123     acc = accuracy_score(labels, preds)
    124     return {

~\Anaconda3\envs\mailbot\lib\site-packages\sklearn\metrics\_classification.py in precision_recall_fscore_support(y_true, y_pred, beta, labels, pos_label, average, warn_for, sample_weight, zero_division)
   1532     if beta < 0:
   1533         raise ValueError("beta should be >=0 in the F-beta score")
-> 1534     labels = _check_set_wise_labels(y_true, y_pred, average, labels, pos_label)
   1535 
   1536     # Calculate tp_sum, pred_sum, true_sum ###

~\Anaconda3\envs\mailbot\lib\site-packages\sklearn\metrics\_classification.py in _check_set_wise_labels(y_true, y_pred, average, labels, pos_label)
   1336         raise ValueError("average has to be one of " + str(average_options))
   1337 
-> 1338     y_type, y_true, y_pred = _check_targets(y_true, y_pred)
   1339     # Convert to Python primitive type to avoid NumPy type / Python str
   1340     # comparison. See https://github.com/numpy/numpy/issues/6784

~\Anaconda3\envs\mailbot\lib\site-packages\sklearn\metrics\_classification.py in _check_targets(y_true, y_pred)
     82     y_pred : array or indicator matrix
     83     """
---> 84     check_consistent_length(y_true, y_pred)
     85     type_true = type_of_target(y_true)
     86     type_pred = type_of_target(y_pred)

~\Anaconda3\envs\mailbot\lib\site-packages\sklearn\utils\validation.py in check_consistent_length(*arrays)
    331         raise ValueError(
    332             "Found input variables with inconsistent numbers of samples: %r"
--> 333             % [int(l) for l in lengths]
    334         )
    335 

ValueError: Found input variables with inconsistent numbers of samples: [4, 3]PYTORCH VERSION: 1.7.1+cpuTRANSFORMERS VERSION: 4.12.3
2021-12-16T14:32:12Z
I have somehow solved the issue - not sure why, but it runs when my custom trainer is the following. I also updated torch to the newest version, i.e. 1.10class TrainerCustom(transformers.Trainer):
    # def __init__(self):
    #     super().__init__()

    def __init__(self, weights, *args, **kwargs):
        super().__init__(*args, **kwargs)

        # initialize weights from argument
        self.weights = weights

    def compute_loss(self, model, inputs, return_outputs=False):
        """
        How the loss is computed by Trainer. By default, all models return the loss in the first element.
        Subclass and override for custom behavior.
        """
        labels = inputs.pop("labels").long()

        outputs = model(**inputs)

        print("LABELS:", labels)

        # Save past state if it exists
        if self.args.past_index >= 0:
            self._past = outputs[self.args.past_index]

        loss_func = torch.nn.CrossEntropyLoss(weight = self.weights.to(labels.device))

        loss = loss_func(outputs.get('logits'), labels)

        print("loss:", loss)

        return (loss, outputs) if return_outputs else loss```
2022-11-14T06:05:51Z
JachymDvorak:ValueError: Found input variables with inconsistent numbers of samplesSounds like the shapes of your labels and predictions are not in alignment. I faced a similar problem while fitting alinear regressionmodel . The problem in my case was, Number of rows in X was not equal to number of rows in y. In most case, x as your feature parameter and y as your predictor. But your feature parameter should not be 1D. So check the shape of x and if it is 1D, then convert it from 1D to 2D.x.reshape(-1,1)Also, you likely get problems because you remove rows containing nulls in X_train and y_train independent of each other. y_train probably has few, or no nulls and X_train probably has some. So when you remove a row in X_train and the same row is not removed in y_train it will cause your data to be unsynced and have different lenghts. Instead you should remove nulls before you separate X and y.