Using select/reordering datasets slows operations down immensely

I am using portions of HF's helpful work in preparing / scoring the SQuAD 2.0 data. The problem I have is that after using `select` to re-ordering the dataset, computations slow down immensely where the total scoring process on 131k training examples would take maybe 3 minutes, now take over an hour.

The below example should be reproducible and I have ran myself down this path because I want to use HF's scoring functions and helpful data preparation, but use my own trainer. The training process uses shuffle and therefore the order I trained on no longer matches the original data set order. So, to score my results correctly, the original data set needs to match the order of the training. This requires that I: (1) collect the index for each row of data emitted during training, and (2) use this index information to re-order the datasets correctly so the orders match when I go to score.


The problem is, the dataset class starts performing very poorly as soon as you start manipulating its order by immense magnitudes.



```
from datasets import load_dataset, load_metric
from transformers import BertTokenizerFast, BertForQuestionAnswering
from elasticsearch import Elasticsearch
import numpy as np
import collections
from tqdm.auto import tqdm
import torch

# from https://colab.research.google.com/github/huggingface/notebooks/blob/master/examples/question_answering.ipynb#scrollTo=941LPhDWeYv-
tokenizer = BertTokenizerFast.from_pretrained('bert-base-uncased')
max_length = 384 # The maximum length of a feature (question and context)
doc_stride = 128 # The authorized overlap between two part of the context when splitting it is needed.
pad_on_right = tokenizer.padding_side == "right"
squad_v2 = True

# from https://colab.research.google.com/github/huggingface/notebooks/blob/master/examples/question_answering.ipynb#scrollTo=941LPhDWeYv-
def prepare_validation_features(examples):
    # Tokenize our examples with truncation and maybe padding, but keep the overflows using a stride. This results
    # in one example possible giving several features when a context is long, each of those features having a
    # context that overlaps a bit the context of the previous feature.
    tokenized_examples = tokenizer(
        examples["question" if pad_on_right else "context"],
        examples["context" if pad_on_right else "question"],
        truncation="only_second" if pad_on_right else "only_first",
        max_length=max_length,
        stride=doc_stride,
        return_overflowing_tokens=True,
        return_offsets_mapping=True,
        padding="max_length",
    )

    # Since one example might give us several features if it has a long context, we need a map from a feature to
    # its corresponding example. This key gives us just that.
    sample_mapping = tokenized_examples.pop("overflow_to_sample_mapping")

    # We keep the example_id that gave us this feature and we will store the offset mappings.
    tokenized_examples["example_id"] = []

    for i in range(len(tokenized_examples["input_ids"])):
        # Grab the sequence corresponding to that example (to know what is the context and what is the question).
        sequence_ids = tokenized_examples.sequence_ids(i)
        context_index = 1 if pad_on_right else 0

        # One example can give several spans, this is the index of the example containing this span of text.
        sample_index = sample_mapping[i]
        tokenized_examples["example_id"].append(examples["id"][sample_index])

        # Set to None the offset_mapping that are not part of the context so it's easy to determine if a token
        # position is part of the context or not.
        tokenized_examples["offset_mapping"][i] = [
            (list(o) if sequence_ids[k] == context_index else None)
            for k, o in enumerate(tokenized_examples["offset_mapping"][i])
        ]

    return tokenized_examples

# from https://colab.research.google.com/github/huggingface/notebooks/blob/master/examples/question_answering.ipynb#scrollTo=941LPhDWeYv-
def postprocess_qa_predictions(examples, features, starting_logits, ending_logits, n_best_size = 20, max_answer_length = 30):
    all_start_logits, all_end_logits = starting_logits, ending_logits
    # Build a map example to its corresponding features.
    example_id_to_index = {k: i for i, k in enumerate(examples["id"])}
    features_per_example = collections.defaultdict(list)

    for i, feature in enumerate(features):
        features_per_example[example_id_to_index[feature["example_id"]]].append(i)

    # The dictionaries we have to fill.
    predictions = collections.OrderedDict()

    # Logging.
    print(f"Post-processing {len(examples)} example predictions split into {len(features)} features.")

    # Let's loop over all the examples!
    for example_index, example in enumerate(tqdm(examples)):
        # Those are the indices of the features associated to the current example.
        feature_indices = features_per_example[example_index]

        min_null_score = None # Only used if squad_v2 is True.
        valid_answers = []

        context = example["context"]
        # Looping through all the features associated to the current example.
        for feature_index in feature_indices:

            # We grab the predictions of the model for this feature.
            start_logits = all_start_logits[feature_index]
            end_logits = all_end_logits[feature_index]
            # This is what will allow us to map some the positions in our logits to span of texts in the original
            # context.
            offset_mapping = features[feature_index]["offset_mapping"]

            # Update minimum null prediction.
            cls_index = features[feature_index]["input_ids"].index(tokenizer.cls_token_id)
            feature_null_score = start_logits[cls_index] + end_logits[cls_index]
            if min_null_score is None or min_null_score < feature_null_score:
                min_null_score = feature_null_score

            # Go through all possibilities for the `n_best_size` greater start and end logits.
            start_indexes = np.argsort(start_logits)[-1 : -n_best_size - 1 : -1].tolist()
            end_indexes = np.argsort(end_logits)[-1 : -n_best_size - 1 : -1].tolist()
            for start_index in start_indexes:
                for end_index in end_indexes:
                    # Don't consider out-of-scope answers, either because the indices are out of bounds or correspond
                    # to part of the input_ids that are not in the context.
                    if (
                        start_index >= len(offset_mapping)
                        or end_index >= len(offset_mapping)
                        or offset_mapping[start_index] is None
                        or offset_mapping[end_index] is None
                    ):
                        continue
                    # Don't consider answers with a length that is either < 0 or > max_answer_length.
                    if end_index < start_index or end_index - start_index + 1 > max_answer_length:
                        continue

                    start_char = offset_mapping[start_index][0]
                    end_char = offset_mapping[end_index][1]
                    valid_answers.append(
                        {
                            "score": start_logits[start_index] + end_logits[end_index],
                            "text": context[start_char: end_char]
                        }
                    )


        if len(valid_answers) > 0:
            best_answer = sorted(valid_answers, key=lambda x: x["score"], reverse=True)[0]
        else:
            # In the very rare edge case we have not a single non-null prediction, we create a fake prediction to avoid
            # failure.
            best_answer = {"text": "", "score": 0.0}

        # Let's pick our final answer: the best one or the null answer (only for squad_v2)
        if not squad_v2:
            predictions[example["id"]] = best_answer["text"]
        else:
            answer = best_answer["text"] if best_answer["score"] > min_null_score else ""
            predictions[example["id"]] = answer

    return predictions



# build base examples, features from training data
examples = load_dataset("squad_v2").shuffle(seed=5)['train']
features = load_dataset("squad_v2").shuffle(seed=5)['train'].map(
    prepare_validation_features,
    batched=True,
    remove_columns=['answers', 'context', 'id', 'question', 'title'])

# sim some shuffled training indices that we want to use to re-order the data to compare how we did
shuffle_idx = np.arange(0, 131754)
np.random.shuffle(shuffle_idx)
# create a new dataset with rows selected following the training shuffle
features = features.select(indices=shuffle_idx)
# get unique example ids to match with the "example" data
id_list = list(dict.fromkeys(features['example_id']))
# now search for their index positions; load elastic search
es = Elasticsearch([{'host': 'localhost'}]).ping()
# add an index to the id column for the examples
examples.add_elasticsearch_index(column='id')
# search the examples for their index position
example_idx = [examples.search(index_name='id', query=i, k=1).indices for i in id_list]
# drop the elastic search
examples.drop_index(index_name='id')
# put examples in the right order
examples = examples.select(indices=example_idx)

# generate some fake data
logits = {'starting_logits': torch.randn(131754, 384), 'ending_logits': torch.randn(131754, 384)}


def score_squad(logits, n_best_size, max_answer):
    # proceed with QA calculation
    final_predictions = postprocess_qa_predictions(examples=examples,
                                                   features=features,
                                                   starting_logits=logits['starting_logits'],
                                                   ending_logits=logits['ending_logits'],
                                                   n_best_size=20,
                                                   max_answer_length=30)
    metric = load_metric("squad_v2")
    formatted_predictions = [{"id": k, "prediction_text": v, "no_answer_probability": 0.0} for k, v in final_predictions.items()]
    references = [{"id": ex["id"], "answers": ex["answers"]} for ex in examples]
    metrics = metric.compute(predictions=formatted_predictions, references=references)
    return metrics

metrics = score_squad(logits, n_best_size=20, max_answer=30)
```















Comments:
You can use `Dataset.flatten_indices()` to make it fast after a select or shuffle.

Thanks for the input! I gave that a try by adding this after my selection / reordering operations, but before the big computation task of `score_squad`

```
examples = examples.flatten_indices()
features = features.flatten_indices()
```

That helped quite a bit!