[Generation] Fix Transition probs
# What does this PR do?

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Fixes #15869

This PR fixes incorrectly computed transition probabilties for beam search.
In beam search it's common to want to know the transition probability between tokens -> see: https://discuss.huggingface.co/t/generation-probabilities-how-to-compute-probabilities-of-output-scores-for-gpt2/3175/15?u=patrickvonplaten

Currently there is a bug for every beam search that ends before `max_length` as discovered by #15869 .

This PR fixes this behavior and adds a couple of tests. 

🚨 **There is a tiny breaking change** in the output format of `beam_indices`. Instead of returning a `tuple(tuple(int))` a `torch.LongTensor` is returned. Since the feature was broken before (`beam_indices` were incorrect), this is hardly a breaking change and necessary to make the functionality more userfriendly and robustu🚨

@patil-suraj @gante , it would be super nice if you could do an in-depth review here also to understand this feature.
**Note:** people do seem to be interested in output scores for generation as can be seen by the large number of views here: https://discuss.huggingface.co/t/generation-probabilities-how-to-compute-probabilities-of-output-scores-for-gpt2/3175

Feel free to drop any question in the PR if you don't understand something or something is unclear - thanks :pray:

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Models:

- albert, bert, xlm: @LysandreJik
- blenderbot, bart, marian, pegasus, encoderdecoder,  t5: @patrickvonplaten, @patil-suraj
- longformer, reformer, transfoxl, xlnet: @patrickvonplaten
- fsmt: @stas00
- funnel: @sgugger
- gpt2: @patrickvonplaten, @LysandreJik
- rag: @patrickvonplaten, @lhoestq
- tensorflow: @LysandreJik

Library:

- benchmarks: @patrickvonplaten
- deepspeed: @stas00
- ray/raytune: @richardliaw, @amogkam
- text generation: @patrickvonplaten
- tokenizers: @n1t0, @LysandreJik
- trainer: @sgugger
- pipelines: @LysandreJik

Documentation: @sgugger

HF projects:

- datasets: [different repo](https://github.com/huggingface/datasets)
- rust tokenizers: [different repo](https://github.com/huggingface/tokenizers)

Examples:

- maintained examples (not research project or legacy): @sgugger, @patil-suraj
- research_projects/bert-loses-patience: @JetRunner
- research_projects/distillation: @VictorSanh

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_The documentation is not available anymore as the PR was closed or merged._<|||||>I'll talk about this feature in more-detail in a tutorial<|||||>Hello,
Regarding the follow up to these 3 posts: https://discuss.huggingface.co/t/generation-probabilities-how-to-compute-probabilities-of-output-scores-for-gpt2/3175/23, https://discuss.huggingface.co/t/retrieving-probability-over-tokens-during-beam-search/21217, https://discuss.huggingface.co/t/get-top-k-tokens-for-each-time-step-instead-of-the-highest-probability-token/14032:

Can you show us, step by step, how to retrieve the probability for each token generated for each prediction in a `transformers.generation_utils.BeamSearchEncoderDecoderOutput`?

Much appreciated.<|||||>Hi @adamkhakhar -- it is in our plans to write a tutorial for that :) It probably won't happen in the next 1 or 2 months, but stay tuned 🙏  <|||||>Hi @patrickvonplaten and @gante; what is the perspective on the tutorial?<|||||>No news yet :)<|||||>Thanks for the quick response @gante. I will stay tuned. Can you tell me whether you can expect the first generated sequence to always have the highest probability?<|||||>@MotzWanted yeah, if you use `num_return_sequences >1` with beam search, the output sequences are sorted by their score (from highest to lowest)<|||||>But if I replicate this [showcase](https://discuss.huggingface.co/t/generation-probabilities-how-to-compute-probabilities-of-output-scores-for-gpt2/3175/26) of @patrickvonplaten to compute the sequence probabilities of the output scores, I don't get that output sequences are sorted by their probability (from highest to lowest). Can you explain to me why this is so @gante?<|||||>@MotzWanted my reply was given in the context of this thread, which is related to `beam_search`. Any call with `do_sample=True`, as in the example you linked, will lose the sorting property.

A working example:
```python
import torch
from transformers import AutoModelForCausalLM
from transformers import AutoTokenizer


gpt2 = AutoModelForCausalLM.from_pretrained("gpt2", return_dict_in_generate=True)
tokenizer = AutoTokenizer.from_pretrained("gpt2")

input_ids = tokenizer("Today is a nice day", return_tensors="pt").input_ids

generated_outputs = gpt2.generate(input_ids, num_return_sequences=3, num_beams=3, output_scores=True)
print(generated_outputs.sequences_scores)
```