EvalPrediction returning one less prediction than label id for each batch
Hi there,I am attempting to recreate R2Bert (see paper here:https://www.aclweb.org/anthology/2020.findings-emnlp.141.pdf) which combines regression and ranking as part of the loss function when training a model to correctly predict an essay score. I have successfully built the model with native Pytorch to train. However, when I use the trainer module all is well when I am training the model, but if I call evaluate or predict methods on the trainer, then I am met by an arrow error which is the result of the EvalPrediction.prediction tensor being of difference length than EvalPrediction.label_id. After some snooping around I noticed that the difference in length turns out to always be the difference in epochs, so for example evaluating over 5 batches I get that the difference is 5 outputs. Any ideas on what might be causing this?Here’s my code, also I use the ASAP dataset but with only 32 essays for each the test, validation and training set, just as a scrap dataset to try and get the model working ( I’ve tried with the full dataset: behaviour is the same _importsfrom transformers import (TrainingArguments,
                          Trainer,
                          AutoConfig,
                          AutoTokenizer, 
                          AutoModel,
                          AdamW,
                          EvalPrediction)
from datasets import load_metric,load_dataset
import torch
from torch import nn
import torch.nn.functional as F
from sklearn.metrics import cohen_kappa_score
import reacquiring datasetmodel_name = 'bert-base-uncased'

path = 'datasets/AES/asap'

dataset_title = 'asap'

# loading dataset
dataset = load_dataset('csv', data_files={'train':[f'{path}/PreProcessed/CsvFiles/{dataset_title}_dev_train.csv'],
                                                'val':[f'{path}/PreProcessed/CsvFiles/{dataset_title}_dev_val.csv'],
                                                'test':[f'{path}/PreProcessed/CsvFiles/{dataset_title}_dev_test.csv']})Tokenizing dataset# tokenizing dataset

tokenizer = AutoTokenizer.from_pretrained(model_name)

def encode_batch(batch):

"""Encodes a batch of input data using the model tokenizer."""

return tokenizer(batch["essay"], max_length=512, truncation=True, padding="max_length")

# Encode the input data

dataset = dataset.map(encode_batch, batched=True)

# labels = normalised scores, domain1_score = original score, essay_set = prompt number the essay belongs to

# will be used to adjust predicted scores to original scoring scale for each essay.

dataset.set_format(type="torch", columns=["input_ids", "attention_mask","essay_set","labels","domain1_score"])Building the model:class R2BERT(nn.Module):

  def __init__(
        self, 
        pretrained_model_name,
        norm_params = None,
    ):
        super().__init__()
        # get bert model
        config = AutoConfig.from_pretrained(pretrained_model_name)
        self.model = AutoModel.from_pretrained(pretrained_model_name,
                                               config=config)
        # add final layer to make score prediction
        self.predictor = nn.Linear(config.hidden_size,1)
        # To be used for calculating kappa metric, by accessing the minimum score and
        # score range for each essay set to get predictions to original scoring range.
        # but not got round to it yet
        self.norm_params = norm_params


  # method for freezing bert layers (using regex to find all layers less than 
  # a specified n_training_layer and then setting requires_grad = False).
  # Done mainly to avoid CUDA: runtime error when training
  def set_trainable_params(self,n_training_layer=None):
    for param_name,param_value in model.named_parameters():
      if n_training_layer:
        layer_num = re.findall(r'\d+',param_name)
        if len(layer_num)>0:
          layer_num = int(layer_num[0])
        else:
          layer_num = 0
        if param_name.startswith('model') and layer_num<n_training_layer:
          param_value.requires_grad = False
      else:
        if param_name.startswith('model'):
          param_value.requires_grad = False

  # Forward pass of the model takes inputs as ••kwargs making it a dictionary.
  # Then the values of keys: 'input_ids' and 'attention_mask' are used to get output of bert
  # Linear layer applied to get score and returned as model output. Dimension of output changed 
  # from [batch size,1] to just batch size to prevent broadcasting error.
  def forward(self,**inputs):
    bert_output = self.model(
        input_ids=inputs['input_ids'],
        attention_mask=inputs['attention_mask'])
    text_representation = bert_output[0][:,0,:]
    batch_size = inputs['input_ids'].size()[0]
    return self.predictor(text_representation).view(batch_size)

# Specific trainer class created to create a custom loss function
class R2Trainer(Trainer):

  def compute_loss(self,model,inputs, return_outputs=False):
    # labels are the scores of the essays
    labels = inputs["labels"]
    # The output of the model is passed through a sigmoid activation function
    # to ensure it is between 0 and 1. This is because the essay scores have been normalised
    # with min max scaling to adjust for different scoring ranges for different prompts.
    outputs = torch.sigmoid(model(**inputs))
    # mean square error used as regression loss
    loss_m = F.mse_loss(outputs,labels)
    # soft max is applied to both predicted and normalised scores (essentially determing the probability
    # that for each essay in the set that it woruld be ranked the highest scoring)
    # This enables the use of the listnet algorithm which is used for ranking loss
    sm_pred_scores = F.softmax(outputs,dim=0)
    sm_gold_scores = F.softmax(labels,dim=0) 
    # The loss for the listnet function is the cross entropy as applied here, this essentially determines 
    # how different the two soft max distrobutions are
    loss_r = torch.sum((-sm_gold_scores*torch.log(sm_pred_scores)))
    # The losses are then added together 
    loss = loss_m + loss_r
    return (loss, outputs) if return_outputs else loss


def compute_accuracy(p):
    #####################################################
    # Here is where the error lies p.predictions returns only 30 
    # predictions for the training arguments and parameters set below
    logits, labels = p.predictions,p.label_ids
    print(p)
    return metric.compute(predictions=logits, references=labels)

model = R2BERT(model_name)
model.set_trainable_params(6)
device = 'cuda' if torch.cuda.is_available() else 'cpu'
model.to(device)

metric = load_metric("pearsonr","spearmanr")

training_args = TrainingArguments(
    learning_rate=4e-5,
    num_train_epochs=2,
    per_device_train_batch_size=16,
    per_device_eval_batch_size=16,
    logging_steps=200,
    output_dir="./training_output",
    overwrite_output_dir=True,
    evaluation_strategy='steps',
    remove_unused_columns=False,
)

trainer = R2Trainer(
    model=model,
    args=training_args,
    train_dataset=dataset["train"],
    eval_dataset=dataset["val"],
    compute_metrics=compute_accuracy,
)Trainingtrainer.train()Output:TrainOutput(global_step=4, training_loss=2.8204991817474365, metrics={'train_runtime': 2.4896, 'train_samples_per_second': 25.707, 'train_steps_per_second': 1.607, 'total_flos': 0.0, 'train_loss': 2.8204991817474365, 'epoch': 2.0})Predicting:trainer.predict(dataset['test'])Output and Error:EvalPrediction(predictions=array([0.6802865 , 0.69348145, 0.7554306 , 0.70484996, 0.7307703 ,
       0.74552727, 0.6842238 , 0.76353663, 0.69672614, 0.7247801 ,
       0.77793705, 0.7025176 , 0.6014939 , 0.6216687 , 0.702473  ,
       0.6444423 , 0.73216194, 0.75792855, 0.7077718 , 0.62824374,
       0.72637045, 0.7813148 , 0.71593434, 0.7130688 , 0.7126326 ,
       0.7286271 , 0.6804262 , 0.7279507 , 0.69572073, 0.72733516],
      dtype=float32), label_ids=array([0.75      , 0.        , 0.75      , 0.6       , 0.6       ,
       0.2       , 0.4       , 1.        , 0.6       , 0.6666667 ,
       0.6363636 , 0.75      , 0.9       , 0.75      , 0.25      ,
       0.56      , 0.75      , 0.6666667 , 0.27272728, 0.5       ,
       1.        , 0.        , 0.44      , 1.        , 0.6       ,
       0.4       , 0.36      , 0.5       , 0.36363637, 0.8181818 ,
       1.        , 0.59090906], dtype=float32))
---------------------------------------------------------------------------
ArrowInvalid                              Traceback (most recent call last)
/usr/local/lib/python3.7/dist-packages/datasets/metric.py in add_batch(self, predictions, references)
    434         try:
--> 435             self.writer.write_batch(batch)
    436         except pa.ArrowInvalid:

10 frames
ArrowInvalid: Column 1 named references expected length 30 but got length 32

During handling of the above exception, another exception occurred:

ValueError                                Traceback (most recent call last)
/usr/local/lib/python3.7/dist-packages/datasets/metric.py in add_batch(self, predictions, references)
    436         except pa.ArrowInvalid:
    437             raise ValueError(
--> 438                 f"Predictions and/or references don't match the expected format.\n"
    439                 f"Expected format: {self.features},\n"
    440                 f"Input predictions: {predictions},\n"

ValueError: Predictions and/or references don't match the expected format.
Expected format: {'predictions': Value(dtype='int32', id=None), 'references': Value(dtype='int32', id=None)},
Input predictions: [0.6802865  0.69348145 0.7554306  0.70484996 0.7307703  0.74552727
 0.6842238  0.76353663 0.69672614 0.7247801  0.77793705 0.7025176
 0.6014939  0.6216687  0.702473   0.6444423  0.73216194 0.75792855
 0.7077718  0.62824374 0.72637045 0.7813148  0.71593434 0.7130688
 0.7126326  0.7286271  0.6804262  0.7279507  0.69572073 0.72733516],
Input references: [0.75       0.         0.75       0.6        0.6        0.2
 0.4        1.         0.6        0.6666667  0.6363636  0.75
 0.9        0.75       0.25       0.56       0.75       0.6666667
 0.27272728 0.5        1.         0.         0.44       1.
 0.6        0.4        0.36       0.5        0.36363637 0.8181818
 1.         0.59090906]Kind Regards,Cameron- `transformers` version: 4.7.0
- Platform: Linux-5.4.104+-x86_64-with-Ubuntu-18.04-bionic
- Python version: 3.7.10
- PyTorch version (GPU?): 1.8.1+cu101 (True)
- Tensorflow version (GPU?): 2.5.0 (True)
- Using GPU in script?: <fill in>
- Using distributed or parallel set-up in script?: <fill in>
2021-06-18T13:53:23Z
hey@cameronstronge, looking at your error i think the problem is that both your predictions and ground truth labels are floats, while yourcompute_accuracyfunction expects integers.if you fix that, doe the problem resolve itself?
2021-06-18T18:54:51Z
Don’t worry figured out my problem in that last post, but I still have the same original issue, despite changing to integers.# output of p.predictions:
[ 2 3 13 5 6 6 3 14 2 23 5 11 2 2 53 2 24 67 3 2 59 5 11 6 55 12 19 24 3 24]

---------------------------------------------------------------------------

ArrowInvalid Traceback (most recent call last)

[/usr/local/lib/python3.7/dist-packages/datasets/metric.py](https://zntzdj4nnfh-496ff2e9c6d22116-0-colab.googleusercontent.com/outputframe.html?vrz=colab-20210616-060129-RC00_379666131#) in add_batch(self, predictions, references) 434 try: --> 435 self.writer.write_batch(batch) 436 except pa.ArrowInvalid:

10 frames

ArrowInvalid: Column 1 named references expected length 30 but got length 32

During handling of the above exception, another exception occurred:

ValueError Traceback (most recent call last)

[/usr/local/lib/python3.7/dist-packages/datasets/metric.py](https://zntzdj4nnfh-496ff2e9c6d22116-0-colab.googleusercontent.com/outputframe.html?vrz=colab-20210616-060129-RC00_379666131#) in add_batch(self, predictions, references) 436 except pa.ArrowInvalid: 437 raise ValueError( --> 438 f"Predictions and/or references don't match the expected format.\n" 439 f"Expected format: {self.features},\n" 440 f"Input predictions: {predictions},\n"

ValueError: Predictions and/or references don't match the expected format. Expected format: {'predictions': Value(dtype='int32', id=None), 'references': Value(dtype='int32', id=None)}, Input predictions: [ 2 3 13 5 6 6 3 14 2 23 5 11 2 2 53 2 24 67 3 2 59 5 11 6 55 12 19 24 3 24], Input references: [ 3 0 3 8 4 2 3 4 8 2 16 3 11 3 1 38 3 2 8 35 3 0 32 4 8 3 28 7 10 20 4 15]In fact done some more snooping and find the first number in the batch is being removed:so this is the output the scores from the model and from the compute_loss function:tensor([ 4,  2,  3, 13,  5,  6,  6,  3, 14,  2, 23,  5, 11,  2,  2, 53],
       dtype=torch.int32)and this is the output at the metrics function[ 2  3 13  5  6  6  3 14  2 23  5 11  2  2 53  2 24 67  3  2 59  5 11  6
 55 12 19 24  3 24]
---------------------
2021-06-18T20:18:13Z
I have come up with a not very pretty solution of appending a 1 to the start of the predictions for each batch.Might be worth investigating further, as seems a bit buggy, but might be my implementation# Here is the method call to calculate the prediction for each essay converted to its corresponding score scale
    #############################################################
    # also here is my unpretty solution for strange behavious of first value disappearing from predictions when evaluation step is called
    predictions = torch.tensor([1]+[self.get_actual_score(score,set_) for score,set_ in zip(scores,sets)], dtype=torch.int)Thanks again,and sorry for so my replies to my own responses in one threadCameron
2021-12-15T12:25:45Z
Hi. I have a similar problem – I get one less class predicted (e.g. y_true = [2, 3, 4], y_hat = [3 ,4]).I modified the Trainer class as following, because I want to add “weight” argument to my CrossEntropyLoss. But, like in your case, I get one less prediction from the .evaluate() method.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):

        labels = inputs.pop("labels")

        outputs = model(**inputs).logits

        self.weights = self.weights.to(labels.device)

        cross_entropy_loss_func = torch.nn.CrossEntropyLoss(weight = self.weights)
   
        loss = cross_entropy_loss_func(outputs, labels.long())
        
        return (loss, outputs) if return_outputs else lossYou would know how to modify the Trainer class so I get rid of the bug of unequal predictions, but keep the weight argument (i.e. modified loss function)?Also, how would I go about using your “dirty” solution, i.e. appending a [1] that gets then removed - where would I add it? I use the Trainer class like you, but I need to append it to the tensor that goes into EvalPrediction, because I want it to return +1  predictions so that the first gets removed (since it’s just a dummy). Not sure where to do that.Thanks!
2022-03-31T03:27:10Z
Hi, I get same question then I find this line code athf/Trainerif isinstance(outputs, dict):
    logits = tuple(v for k, v in outputs.items() if k not in ignore_keys + ["loss"])
else:
    logits = outputs[1:]So, this will discard the firsrt element if your outputs is not a dictionary. My original outputs is a tensor and I wrap it to a dictionary to solve the question.
2023-08-03T16:33:19Z
Hi all,I’m doing some tests to better understand the transformers :adaptation of a basic pytorch model to transformer (config, pretrained…)use a custom loss (just L1Loss instead of MSELoss) for regressionuse of a custom metric (a basic mse just for fun)I’m facing the same issue with a custom model. So I transformed the output of my model to a dictionnary (not a tuple) and I get the same deletion of the first row per batch… any idea ?class MyConfig(PretrainedConfig):model_type = ‘mymodel’definit(self, layer_size = 20, **kwargs):super().init(**kwargs)self.layer_size = layer_sizeclass MyModel(PreTrainedModel):config_class = MyConfigdefinit(self, config):super().init(config)self.config = configself.linear1 = nn.Linear(512, self.config.layer_size)self.linear2 = nn.Linear(self.config.layer_size, 1)def forward(self,input_ids,labels = None):x = input_ids.to(torch.float32)x = self.linear1(x)x = self.linear2(x)return {“input_ids”:x,“labels”:labels}def compute_metrics(eval_pred):predictions, labels = eval_predmetric = mean_squared_error(labels, predictions, squared=False)return {“mse”: metric}class RegressionTrainer(Trainer):def compute_loss(self, model, inputs, return_outputs=False):labels = inputs[‘labels’]outputs = model(**inputs)logits = outputs[‘input_ids’]loss_fct = nn.L1Loss()loss = loss_fct(logits.squeeze(), labels.squeeze())return (loss, logits) if return_outputs else lossFor information, the datasets :print(“data_loader_summaries_train:\n”,data_loader_summaries_train)print(“data_loader_summaries_val:\n”,data_loader_summaries_val)data_loader_summaries_train:Dataset({features: [‘input_ids’, ‘labels’],num_rows: 200})data_loader_summaries_val:Dataset({features: [‘input_ids’, ‘labels’],num_rows: 100})config = MyConfig(4)model2 = MyModel(config)args = TrainingArguments(do_train = True,do_predict  = True,report_to   = ‘none’,label_names = [‘labels’],per_device_eval_batch_size = 20,per_device_train_batch_size = 20,output_dir  = ‘/’,learning_rate = 0.001,num_train_epochs = 3,save_strategy  = “epoch”,evaluation_strategy = “epoch”,greater_is_better  = False,)trainer = RegressionTrainer(args  = args,model   = model2,train_dataset  = data_loader_summaries_train,eval_dataset  = data_loader_summaries_val,compute_metrics = compute_metrics,)trainer.train()=> ValueError: Found input variables with inconsistent numbers of samples: [100, 95]5 batchs => 100 - 5 …
2024-06-19T16:25:54Z
The issue is coming because in the compute_loss function you  output tensor instead of dict in hf Trainer the first sample is removed if it is not a dictionary.referencehere:if isinstance(outputs, dict):
    logits = tuple(v for k, v in outputs.items() if k not in ignore_keys + ["loss"])
else:
    logits = outputs[1:]I solver this issue like this:class CustomTrainer(Trainer):

    def compute_loss(self, model, inputs, return_outputs=False):
        outputs = model(inputs['input_ids'], inputs['attention_mask'])
        
        loss = loss_fn(outputs, inputs['target'])
        return (loss, {"label": outputs}) if return_outputs else losshere i return output in the form of dictionary and this solves the issue for me