[Flax Examples] Seq2Seq ASR Fine-Tuning Script (#21764)

* from seq2seq speech

* [Flax] Example script for speech seq2seq

* tests and fixes

* make style

* fix: label padding tokens

* fix: label padding tokens over list

* update ln names for Whisper

* try datasets iter loader

* create readme and append results

* style

* make style

* adjust lr

* use pt dataloader

* make fast

* pin gen max len

* finish

* add pt to requirements for test

* fix pt -> torch

* add accelerate

examples/flax/_tests_requirements.txt

@@ -5,4 +5,6 @@ nltk
 rouge-score
 seqeval
 tensorboard
-evaluate >= 0.2.0
+evaluate >= 0.2.0
\ No newline at end of file
+torch
+accelerate
\ No newline at end of file

examples/flax/speech-recognition/README.md

+<!---
+Copyright 2023 The HuggingFace Team. All rights reserved.
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+    http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+-->
+
+# Automatic Speech Recognition - Flax Examples
+
+## Sequence to Sequence
+
+The script [`run_flax_speech_recognition_seq2seq.py`](https://github.com/huggingface/transformers/blob/main/examples/flax/speech-recognition/run_flax_speech_recognition_seq2seq.py) 
+can be used to fine-tune any [Flax Speech Sequence-to-Sequence Model](https://huggingface.co/docs/transformers/main/en/model_doc/auto#transformers.FlaxAutoModelForSpeechSeq2Seq) 
+for automatic speech recognition on one of the [official speech recognition datasets](https://huggingface.co/datasets?task_ids=task_ids:automatic-speech-recognition) 
+or a custom dataset. This includes the Whisper model from OpenAI, or a warm-started Speech-Encoder-Decoder Model, 
+an example for which is included below.
+
+### Whisper Model
+
+We can load all components of the Whisper model directly from the pretrained checkpoint, including the pretrained model 
+weights, feature extractor and tokenizer. We simply have to specify the id of fine-tuning dataset and the necessary
+training hyperparameters.
+
+The following example shows how to fine-tune the [Whisper small](https://huggingface.co/openai/whisper-small) checkpoint 
+on the Hindi subset of the [Common Voice 13](https://huggingface.co/datasets/mozilla-foundation/common_voice_13_0) dataset.
+Note that before running this script you must accept the dataset's [terms of use](https://huggingface.co/datasets/mozilla-foundation/common_voice_13_0) 
+and register your Hugging Face Hub token on your device by running `huggingface-hub login`.
+
+```bash
+python run_flax_speech_recognition_seq2seq.py \
+	--model_name_or_path="openai/whisper-small" \
+	--dataset_name="mozilla-foundation/common_voice_13_0" \
+	--dataset_config_name="hi" \
+	--language="hindi" \
+	--train_split_name="train+validation" \
+	--eval_split_name="test" \
+	--output_dir="./whisper-small-hi-flax" \
+	--per_device_train_batch_size="16" \
+	--per_device_eval_batch_size="16" \
+	--num_train_epochs="10" \
+	--learning_rate="1e-4" \
+	--warmup_steps="500" \
+	--logging_steps="25" \
+	--generation_max_length="40" \
+	--preprocessing_num_workers="32" \
+	--dataloader_num_workers="32" \
+	--max_duration_in_seconds="30" \
+	--text_column_name="sentence" \
+	--overwrite_output_dir \
+	--do_train \
+	--do_eval \
+	--predict_with_generate \
+	--push_to_hub \
+	--use_auth_token
+```
+
+On a TPU v4-8, training should take approximately 25 minutes, with a final cross-entropy loss of 0.02 and word error 
+rate of **34%**. See the checkpoint [sanchit-gandhi/whisper-small-hi-flax](https://huggingface.co/sanchit-gandhi/whisper-small-hi-flax)
+for an example training run.

examples/flax/speech-recognition/requirements.txt

+datasets[audio]>=2.14.0
+jax>=0.3.6
+jaxlib>=0.3.6
+flax>=0.4.1
+optax>=0.0.8
+torch>=1.9.0
+jiwer
+evaluate

examples/flax/speech-recognition/run_flax_speech_recognition_seq2seq.py

+#!/usr/bin/env python
+# coding=utf-8
+# Copyright 2023 The HuggingFace Inc. team. All rights reserved.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+"""
+Fine-tuning the Flax library models for sequence to sequence speech recognition.
+"""
+# You can also adapt this script on your own sequence to sequence task. Pointers for this are left as comments.
+
+import logging
+import os
+import sys
+import time
+from dataclasses import field
+from functools import partial
+from pathlib import Path
+from typing import Any, Callable, Dict, List, Optional, Union
+
+import datasets
+import evaluate
+import flax
+import jax
+import jax.numpy as jnp
+import numpy as np
+import optax
+from datasets import DatasetDict, load_dataset
+from flax import jax_utils, traverse_util
+from flax.jax_utils import pad_shard_unpad, unreplicate
+from flax.training import train_state
+from flax.training.common_utils import get_metrics, onehot, shard, shard_prng_key
+from huggingface_hub import Repository, create_repo
+from torch.utils.data import DataLoader
+from tqdm import tqdm
+
+import transformers
+from transformers import (
+    AutoConfig,
+    AutoFeatureExtractor,
+    AutoProcessor,
+    AutoTokenizer,
+    FlaxAutoModelForSpeechSeq2Seq,
+    HfArgumentParser,
+    Seq2SeqTrainingArguments,
+    is_tensorboard_available,
+)
+from transformers.file_utils import get_full_repo_name
+from transformers.utils import check_min_version, send_example_telemetry
+from transformers.utils.versions import require_version
+
+
+# Will error if the minimal version of Transformers is not installed. Remove at your own risk.
+check_min_version("4.32.0.dev0")
+
+require_version("datasets>=2.14.0", "To fix: pip install -r examples/flax/speech-recogintion/requirements.txt")
+
+logger = logging.getLogger(__name__)
+
+
+@flax.struct.dataclass
+class ModelArguments:
+    """
+    Arguments pertaining to which model/config/tokenizer we are going to fine-tune from.
+    """
+
+    model_name_or_path: str = field(
+        metadata={"help": "Path to pretrained model or model identifier from huggingface.co/models"}
+    )
+    config_name: Optional[str] = field(
+        default=None, metadata={"help": "Pretrained config name or path if not the same as model_name"}
+    )
+    tokenizer_name: Optional[str] = field(
+        default=None, metadata={"help": "Pretrained tokenizer name or path if not the same as model_name"}
+    )
+    feature_extractor_name: Optional[str] = field(
+        default=None, metadata={"help": "feature extractor name or path if not the same as model_name"}
+    )
+    cache_dir: Optional[str] = field(
+        default=None,
+        metadata={"help": "Where to store the pretrained models downloaded from huggingface.co"},
+    )
+    use_fast_tokenizer: bool = field(
+        default=True,
+        metadata={"help": "Whether to use one of the fast tokenizer (backed by the tokenizers library) or not."},
+    )
+    model_revision: str = field(
+        default="main",
+        metadata={"help": "The specific model version to use (can be a branch name, tag name or commit id)."},
+    )
+    use_auth_token: bool = field(
+        default=False,
+        metadata={
+            "help": "Will use the token generated when running `transformers-cli login` (necessary to use this script "
+            "with private models)."
+        },
+    )
+    dtype: Optional[str] = field(
+        default="float32",
+        metadata={
+            "help": (
+                "Floating-point format in which the model weights should be initialized and trained. Choose one of"
+                " `[float32, float16, bfloat16]`."
+            )
+        },
+    )
+    num_beams: Optional[int] = field(
+        default=None,
+        metadata={
+            "help": (
+                "Number of beams to use for evaluation. This argument will be passed to `model.generate`, "
+                "which is used during evaluation."
+            )
+        },
+    )
+
+
+@flax.struct.dataclass
+class DataTrainingArguments:
+    """
+    Arguments pertaining to what data we are going to input our model for training and eval.
+    """
+
+    dataset_name: str = field(
+        default=None, metadata={"help": "The name of the dataset to use (via the datasets library)."}
+    )
+    dataset_config_name: Optional[str] = field(
+        default=None, metadata={"help": "The configuration name of the dataset to use (via the datasets library)."}
+    )
+    text_column: Optional[str] = field(
+        default=None,
+        metadata={"help": "The name of the column in the datasets containing the full texts (for summarization)."},
+    )
+    dataset_cache_dir: Optional[str] = field(
+        default=None, metadata={"help": "Path to cache directory for saving and loading datasets"}
+    )
+    overwrite_cache: bool = field(
+        default=False, metadata={"help": "Overwrite the cached training and evaluation sets"}
+    )
+    preprocessing_num_workers: Optional[int] = field(
+        default=None,
+        metadata={"help": "The number of processes to use for the preprocessing."},
+    )
+    max_train_samples: Optional[int] = field(
+        default=None,
+        metadata={
+            "help": "For debugging purposes or quicker training, truncate the number of training examples to this "
+            "value if set."
+        },
+    )
+    max_eval_samples: Optional[int] = field(
+        default=None,
+        metadata={
+            "help": "For debugging purposes or quicker training, truncate the number of evaluation examples to this "
+            "value if set."
+        },
+    )
+    audio_column_name: str = field(
+        default="audio",
+        metadata={"help": "The name of the dataset column containing the audio data. Defaults to 'audio'"},
+    )
+    text_column_name: str = field(
+        default="text",
+        metadata={"help": "The name of the dataset column containing the text data. Defaults to 'text'"},
+    )
+    max_duration_in_seconds: float = field(
+        default=20.0,
+        metadata={"help": "Filter audio files that are longer than `max_duration_in_seconds` seconds"},
+    )
+    min_duration_in_seconds: float = field(
+        default=0.0,
+        metadata={"help": "Filter audio files that are shorter than `min_duration_in_seconds` seconds"},
+    )
+    max_label_length: float = field(
+        default=128,
+        metadata={"help": "Truncate transcriptions that are longer `max_eval_length` tokens."},
+    )
+    pad_input_to_multiple_of: Optional[int] = field(
+        default=None,
+        metadata={
+            "help": "If set will pad the input sequence to a multiple of the provided value. "
+            "This is important to avoid triggering recompilations on TPU. If unspecified, will default to padding the inputs to max length."
+        },
+    )
+    pad_target_to_multiple_of: Optional[int] = field(
+        default=None,
+        metadata={
+            "help": "If set will pad the target sequence to a multiple of the provided value. "
+            "This is important to avoid triggering recompilations on TPU. If unspecified, will default to padding the targets to max length."
+        },
+    )
+    preprocessing_only: bool = field(
+        default=False,
+        metadata={
+            "help": "Whether to only do data preprocessing and skip training. "
+            "This is especially useful when data preprocessing errors out in distributed training due to timeout. "
+            "In this case, one should run the preprocessing in a non-distributed setup with `preprocessing_only=True` "
+            "so that the cached datasets can consequently be loaded in distributed training"
+        },
+    )
+    train_split_name: str = field(
+        default="train",
+        metadata={
+            "help": "The name of the training data set split to use (via the datasets library). Defaults to 'train'"
+        },
+    )
+    eval_split_name: str = field(
+        default="validation",
+        metadata={
+            "help": "The name of the evaluation data set split to use (via the datasets library). Defaults to 'validation'"
+        },
+    )
+    do_lower_case: bool = field(
+        default=True,
+        metadata={"help": "Whether the target text should be lower cased."},
+    )
+    language: str = field(
+        default=None,
+        metadata={
+            "help": (
+                "Language for multilingual fine-tuning. This argument should be set for multilingual fine-tuning "
+                "only. For English speech recognition, it should be set to `None`."
+            )
+        },
+    )
+    task: str = field(
+        default="transcribe",
+        metadata={"help": "Task, either `transcribe` for speech recognition or `translate` for speech translation."},
+    )
+
+
+def shift_tokens_right(label_ids: np.array, decoder_start_token_id: int) -> np.ndarray:
+    """
+    Shift label ids one token to the right.
+    """
+    shifted_label_ids = np.zeros_like(label_ids)
+    shifted_label_ids[:, 1:] = label_ids[:, :-1]
+    shifted_label_ids[:, 0] = decoder_start_token_id
+
+    return shifted_label_ids
+
+
+@flax.struct.dataclass
+class FlaxDataCollatorSpeechSeq2SeqWithPadding:
+    """
+    Data collator that will dynamically pad the inputs received.
+    Args:
+        processor ([`Wav2Vec2Processor`])
+            The processor used for proccessing the data.
+        decoder_start_token_id (:obj: `int`)
+            The begin-of-sentence of the decoder.
+        input_padding (:obj:`bool`, :obj:`str` or :class:`~transformers.tokenization_utils_base.PaddingStrategy`, `optional`, defaults to :obj:`True`):
+            Select a strategy to pad the returned input sequences (according to the model's padding side and padding index)
+            among:
+            * :obj:`True` or :obj:`'longest'`: Pad to the longest sequence in the batch (or no padding if only a single
+              sequence if provided).
+            * :obj:`'max_length'`: Pad to a maximum length specified with the argument :obj:`max_length` or to the
+              maximum acceptable input length for the model if that argument is not provided.
+            * :obj:`False` or :obj:`'do_not_pad'` (default): No padding (i.e., can output a batch with sequences of
+              different lengths).
+        target_padding (:obj:`bool`, :obj:`str` or :class:`~transformers.tokenization_utils_base.PaddingStrategy`, `optional`, defaults to :obj:`True`):
+            Select a strategy to pad the returned target sequences (according to the model's padding side and padding index).
+            See above for details.
+        max_input_length (:obj:`float`, `optional`):
+            Maximum length of the ``input_values`` of the returned list and optionally padding length (see above).
+        max_target_length (:obj:`int`, `optional`):
+            Maximum length of the ``labels`` of the returned list and optionally padding length (see above).
+        pad_input_to_multiple_of (:obj:`int`, `optional`):
+            If set will pad the input sequence to a multiple of the provided value.
+            This is especially useful to enable the use of Tensor Cores on NVIDIA hardware with compute capability >=
+            7.5 (Volta).
+        pad_target_to_multiple_of (:obj:`int`, `optional`):
+            If set will pad the target sequence to a multiple of the provided value.
+            This is especially useful to enable the use of Tensor Cores on NVIDIA hardware with compute capability >=
+            7.5 (Volta).
+    """
+
+    processor: Any
+    decoder_start_token_id: int
+    input_padding: Union[bool, str] = "longest"
+    target_padding: Union[bool, str] = "max_length"
+    max_input_length: Optional[float] = None
+    max_target_length: Optional[int] = None
+    pad_input_to_multiple_of: Optional[int] = None
+    pad_target_to_multiple_of: Optional[int] = None
+
+    def __call__(self, features: List[Dict[str, Union[List[int], np.ndarray]]]) -> Dict[str, np.ndarray]:
+        # split inputs and labels since they have to be of different lengths and need
+        # different padding methods
+        model_input_name = self.processor.model_input_names[0]
+
+        # dataloader returns a list of features which we convert to a dict
+        input_features = {model_input_name: [feature[model_input_name] for feature in features]}
+        label_features = {"input_ids": [feature["labels"] for feature in features]}
+
+        # reformat list to dict and set to pytorch format
+        batch = self.processor.feature_extractor.pad(
+            input_features,
+            max_length=self.max_input_length,
+            padding=self.input_padding,
+            pad_to_multiple_of=self.pad_input_to_multiple_of,
+            return_tensors="np",
+        )
+
+        labels_batch = self.processor.tokenizer.pad(
+            label_features,
+            max_length=self.max_target_length,
+            padding=self.target_padding,
+            pad_to_multiple_of=self.pad_target_to_multiple_of,
+            return_tensors="np",
+        )
+
+        # if bos token is appended in previous tokenization step,
+        # cut bos token here as it's append later anyways
+        labels = labels_batch["input_ids"]
+        if (labels[:, 0] == self.decoder_start_token_id).all().item():
+            labels = labels[:, 1:]
+            labels_batch.attention_mask = labels_batch.attention_mask[:, 1:]
+
+        decoder_input_ids = shift_tokens_right(labels, self.decoder_start_token_id)
+
+        # replace padding with -100 to ignore correctly when computing the loss
+        labels = np.ma.array(labels, mask=np.not_equal(labels_batch.attention_mask, 1))
+        labels = labels.filled(fill_value=-100)
+
+        batch["labels"] = labels
+        batch["decoder_input_ids"] = decoder_input_ids
+
+        return batch
+
+
+class TrainState(train_state.TrainState):
+    dropout_rng: jnp.ndarray
+
+    def replicate(self):
+        return jax_utils.replicate(self).replace(dropout_rng=shard_prng_key(self.dropout_rng))
+
+
+def write_metric(summary_writer, train_metrics, eval_metrics, train_time, step):
+    summary_writer.scalar("train_time", train_time, step)
+
+    train_metrics = get_metrics(train_metrics)
+    for key, vals in train_metrics.items():
+        tag = f"train_{key}"
+        for i, val in enumerate(vals):
+            summary_writer.scalar(tag, val, step - len(vals) + i + 1)
+
+    for metric_name, value in eval_metrics.items():
+        summary_writer.scalar(f"eval_{metric_name}", value, step)
+
+
+def create_learning_rate_fn(
+    num_train_steps: int, num_warmup_steps: int, learning_rate: float
+) -> Callable[[int], jnp.array]:
+    """Returns a linear warmup, linear_decay learning rate function."""
+    warmup_fn = optax.linear_schedule(init_value=0.0, end_value=learning_rate, transition_steps=num_warmup_steps)
+    decay_fn = optax.linear_schedule(
+        init_value=learning_rate, end_value=0, transition_steps=num_train_steps - num_warmup_steps
+    )
+    schedule_fn = optax.join_schedules(schedules=[warmup_fn, decay_fn], boundaries=[num_warmup_steps])
+    return schedule_fn
+
+
+def main():
+    # 1. Parse input arguments
+    # See all possible arguments in src/transformers/training_args.py
+    # or by passing the --help flag to this script.
+    # We now keep distinct sets of args, for a cleaner separation of concerns.
+    parser = HfArgumentParser((ModelArguments, DataTrainingArguments, Seq2SeqTrainingArguments))
+
+    if len(sys.argv) == 2 and sys.argv[1].endswith(".json"):
+        # If we pass only one argument to the script and it's the path to a json file,
+        # let's parse it to get our arguments.
+        model_args, data_args, training_args = parser.parse_json_file(json_file=os.path.abspath(sys.argv[1]))
+    else:
+        model_args, data_args, training_args = parser.parse_args_into_dataclasses()
+
+    # Sending telemetry. Tracking the example usage helps us better allocate resources to maintain them. The
+    # information sent is the one passed as arguments along with your JAX/Flax versions.
+    send_example_telemetry("run_speech_recognition_seq2seq", model_args, data_args, framework="flax")
+
+    # 2. Setup logging
+    # Make one log on every process with the configuration for debugging.
+    logging.basicConfig(
+        format="%(asctime)s - %(levelname)s - %(name)s - %(message)s",
+        datefmt="%m/%d/%Y %H:%M:%S",
+        handlers=[logging.StreamHandler(sys.stdout)],
+    )
+    # Set the verbosity to info of the Transformers logger.
+    # We only want one process per machine to log things on the screen.
+    logger.setLevel(logging.INFO if jax.process_index() == 0 else logging.ERROR)
+    if jax.process_index() == 0:
+        datasets.utils.logging.set_verbosity_warning()
+        transformers.utils.logging.set_verbosity_info()
+    else:
+        datasets.utils.logging.set_verbosity_error()
+        transformers.utils.logging.set_verbosity_error()
+
+    logger.info("Training/evaluation parameters %s", training_args)
+
+    # Check the output dir is valid
+    if (
+        os.path.exists(training_args.output_dir)
+        and os.listdir(training_args.output_dir)
+        and training_args.do_train
+        and not training_args.overwrite_output_dir
+    ):
+        raise ValueError(
+            f"Output directory ({training_args.output_dir}) already exists and is not empty."
+            "Use `--overwrite_output_dir` to overcome."
+        )
+
+    # Handle the repository creation
+    if training_args.push_to_hub:
+        if training_args.hub_model_id is None:
+            repo_name = get_full_repo_name(
+                Path(training_args.output_dir).absolute().name, token=training_args.hub_token
+            )
+        else:
+            repo_name = training_args.hub_model_id
+        create_repo(repo_name, exist_ok=True, token=training_args.hub_token)
+        repo = Repository(training_args.output_dir, clone_from=repo_name, token=training_args.hub_token)
+
+    # 3. Load dataset
+    raw_datasets = DatasetDict()
+
+    if training_args.do_train:
+        raw_datasets["train"] = load_dataset(
+            data_args.dataset_name,
+            data_args.dataset_config_name,
+            split=data_args.train_split_name,
+            cache_dir=data_args.dataset_cache_dir,
+            token=True if model_args.use_auth_token else None,
+        )
+
+    if training_args.do_eval:
+        raw_datasets["eval"] = load_dataset(
+            data_args.dataset_name,
+            data_args.dataset_config_name,
+            split=data_args.eval_split_name,
+            cache_dir=data_args.dataset_cache_dir,
+            token=True if model_args.use_auth_token else None,
+        )
+
+    if not training_args.do_train and not training_args.do_eval:
+        raise ValueError(
+            "Cannot not train and not do evaluation. At least one of training or evaluation has to be performed."
+        )
+
+    if data_args.audio_column_name not in next(iter(raw_datasets.values())).column_names:
+        raise ValueError(
+            f"--audio_column_name '{data_args.audio_column_name}' not found in dataset '{data_args.dataset_name}'. "
+            "Make sure to set `--audio_column_name` to the correct audio column - one of "
+            f"{', '.join(next(iter(raw_datasets.values())).column_names)}."
+        )
+
+    if data_args.text_column_name not in next(iter(raw_datasets.values())).column_names:
+        raise ValueError(
+            f"--text_column_name {data_args.text_column_name} not found in dataset '{data_args.dataset_name}'. "
+            "Make sure to set `--text_column_name` to the correct text column - one of "
+            f"{', '.join(next(iter(raw_datasets.values())).column_names)}."
+        )
+
+    # 5. Load pretrained model, tokenizer, and feature extractor
+    config = AutoConfig.from_pretrained(
+        model_args.config_name if model_args.config_name else model_args.model_name_or_path,
+        cache_dir=model_args.cache_dir,
+        revision=model_args.model_revision,
+        token=True if model_args.use_auth_token else None,
+    )
+    feature_extractor = AutoFeatureExtractor.from_pretrained(
+        model_args.feature_extractor_name if model_args.feature_extractor_name else model_args.model_name_or_path,
+        cache_dir=model_args.cache_dir,
+        revision=model_args.model_revision,
+        token=True if model_args.use_auth_token else None,
+    )
+    tokenizer = AutoTokenizer.from_pretrained(
+        model_args.tokenizer_name if model_args.tokenizer_name else model_args.model_name_or_path,
+        cache_dir=model_args.cache_dir,
+        use_fast=model_args.use_fast_tokenizer,
+        revision=model_args.model_revision,
+        token=True if model_args.use_auth_token else None,
+    )
+
+    model = FlaxAutoModelForSpeechSeq2Seq.from_pretrained(
+        model_args.model_name_or_path,
+        config=config,
+        dtype=getattr(jnp, model_args.dtype),
+        cache_dir=model_args.cache_dir,
+        revision=model_args.model_revision,
+        token=True if model_args.use_auth_token else None,
+    )
+
+    if model.config.decoder_start_token_id is None:
+        raise ValueError("Make sure that `config.decoder_start_token_id` is correctly defined")
+
+    # 6. Resample speech dataset: `datasets` takes care of automatically loading and resampling the audio,
+    # so we just need to set the correct target sampling rate.
+    raw_datasets = raw_datasets.cast_column(
+        data_args.audio_column_name, datasets.features.Audio(sampling_rate=feature_extractor.sampling_rate)
+    )
+
+    # 7. Preprocessing the datasets.
+    # We need to read the audio files as arrays and tokenize the targets.
+    max_input_length = int(data_args.max_duration_in_seconds * feature_extractor.sampling_rate)
+    min_input_length = int(data_args.min_duration_in_seconds * feature_extractor.sampling_rate)
+    max_label_length = (
+        data_args.max_label_length if data_args.max_label_length is not None else model.config.max_length
+    )
+    pad_input_to_multiple_of = data_args.pad_input_to_multiple_of
+    pad_target_to_multiple_of = data_args.pad_target_to_multiple_of
+    audio_column_name = data_args.audio_column_name
+    num_workers = data_args.preprocessing_num_workers
+    text_column_name = data_args.text_column_name
+    model_input_name = feature_extractor.model_input_names[0]
+    do_lower_case = data_args.do_lower_case
+
+    if training_args.do_train and data_args.max_train_samples is not None:
+        raw_datasets["train"] = raw_datasets["train"].select(range(data_args.max_train_samples))
+
+    if training_args.do_eval and data_args.max_eval_samples is not None:
+        raw_datasets["eval"] = raw_datasets["eval"].select(range(data_args.max_eval_samples))
+
+    if data_args.language is not None:
+        # We only need to set the task id when the language is specified (i.e. in a multilingual setting)
+        tokenizer.set_prefix_tokens(language=data_args.language, task=data_args.task)
+
+    def prepare_dataset(batch):
+        # process audio
+        sample = batch[audio_column_name]
+        inputs = feature_extractor(sample["array"], sampling_rate=sample["sampling_rate"])
+        # process audio length
+        batch[model_input_name] = inputs.get(model_input_name)[0]
+        batch["input_length"] = len(sample["array"])
+
+        # process targets
+        input_str = batch[text_column_name].lower() if do_lower_case else batch[text_column_name]
+        batch["labels"] = tokenizer(input_str).input_ids
+        return batch
+
+    vectorized_datasets = raw_datasets.map(
+        prepare_dataset,
+        remove_columns=next(iter(raw_datasets.values())).column_names,
+        num_proc=num_workers,
+        desc="preprocess train dataset",
+    )
+
+    # filter training data with inputs longer than max_input_length
+    def is_audio_in_length_range(length):
+        return min_input_length < length < max_input_length
+
+    vectorized_datasets = vectorized_datasets.filter(
+        is_audio_in_length_range,
+        num_proc=num_workers,
+        input_columns=["input_length"],
+    )
+
+    # for large datasets it is advised to run the preprocessing on a
+    # single machine first with `args.preprocessing_only` since there will mostly likely
+    # be a timeout when running the script in distributed mode.
+    # In a second step `args.preprocessing_only` can then be set to `False` to load the
+    # cached dataset
+    if data_args.preprocessing_only:
+        cache = {k: v.cache_files for k, v in vectorized_datasets.items()}
+        logger.info(f"Data preprocessing finished. Files cached at {cache}.")
+        return
+
+    # 8. Load Metric
+    metric = evaluate.load("wer")
+
+    def compute_metrics(preds, labels):
+        # replace padded labels by the padding token
+        for idx in range(len(labels)):
+            labels[idx][labels[idx] == -100] = tokenizer.pad_token_id
+
+        pred_str = tokenizer.batch_decode(preds, skip_special_tokens=True)
+        # we do not want to group tokens when computing the metrics
+        label_str = tokenizer.batch_decode(labels, skip_special_tokens=True)
+
+        wer = metric.compute(predictions=pred_str, references=label_str)
+        return {"wer": wer}
+
+    # 9. Save feature extractor, tokenizer and config
+    feature_extractor.save_pretrained(training_args.output_dir)
+    tokenizer.save_pretrained(training_args.output_dir)
+    config.save_pretrained(training_args.output_dir)
+
+    processor = AutoProcessor.from_pretrained(training_args.output_dir)
+
+    data_collator = FlaxDataCollatorSpeechSeq2SeqWithPadding(
+        processor=processor,
+        decoder_start_token_id=model.config.decoder_start_token_id,
+        input_padding="longest",
+        target_padding="longest",
+        max_target_length=max_label_length,
+        pad_input_to_multiple_of=pad_input_to_multiple_of,
+        pad_target_to_multiple_of=pad_target_to_multiple_of if pad_target_to_multiple_of else max_label_length,
+    )
+
+    # Enable tensorboard only on the master node
+    has_tensorboard = is_tensorboard_available()
+    if has_tensorboard and jax.process_index() == 0:
+        try:
+            from flax.metrics.tensorboard import SummaryWriter
+
+            summary_writer = SummaryWriter(log_dir=Path(training_args.output_dir))
+        except ImportError as ie:
+            has_tensorboard = False
+            logger.warning(
+                f"Unable to display metrics through TensorBoard because some package are not installed: {ie}"
+            )
+    else:
+        logger.warning(
+            "Unable to display metrics through TensorBoard because the package is not installed: "
+            "Please run pip install tensorboard to enable."
+        )
+
+    # Initialize our training
+    rng = jax.random.PRNGKey(training_args.seed)
+    rng, dropout_rng = jax.random.split(rng)
+
+    # Store some constant
+    num_epochs = int(training_args.num_train_epochs)
+    train_batch_size = int(training_args.per_device_train_batch_size) * jax.device_count()
+    per_device_eval_batch_size = int(training_args.per_device_eval_batch_size)
+    eval_batch_size = per_device_eval_batch_size * jax.device_count()
+    steps_per_epoch = len(vectorized_datasets["train"]) // train_batch_size
+    total_train_steps = steps_per_epoch * num_epochs
+
+    # Create learning rate schedule
+    linear_decay_lr_schedule_fn = create_learning_rate_fn(
+        len(vectorized_datasets["train"]),
+        training_args.warmup_steps,
+        training_args.learning_rate,
+    )
+
+    # We use Optax's "masking" functionality to not apply weight decay
+    # to bias and LayerNorm scale parameters. decay_mask_fn returns a
+    # mask boolean with the same structure as the parameters.
+    # The mask is True for parameters that should be decayed.
+    def decay_mask_fn(params):
+        flat_params = traverse_util.flatten_dict(params)
+        # find out all LayerNorm parameters
+        layer_norm_candidates = ["layer_norm", "self_attn_layer_norm", "final_layer_norm", "encoder_attn_layer_norm"]
+        layer_norm_named_params = {
+            layer[-2:]
+            for layer_norm_name in layer_norm_candidates
+            for layer in flat_params.keys()
+            if layer_norm_name in "".join(layer).lower()
+        }
+        flat_mask = {path: (path[-1] != "bias" and path[-2:] not in layer_norm_named_params) for path in flat_params}
+        return traverse_util.unflatten_dict(flat_mask)
+
+    # create adam optimizer
+    adamw = optax.adamw(
+        learning_rate=linear_decay_lr_schedule_fn,
+        b1=training_args.adam_beta1,
+        b2=training_args.adam_beta2,
+        eps=training_args.adam_epsilon,
+        weight_decay=training_args.weight_decay,
+        mask=decay_mask_fn,
+    )
+
+    # Setup train state
+    state = TrainState.create(apply_fn=model.__call__, params=model.params, tx=adamw, dropout_rng=dropout_rng)
+
+    # label smoothed cross entropy
+    def loss_fn(logits, labels, label_smoothing_factor=0.0):
+        """
+        The label smoothing implementation is adapted from Flax's official example:
+        https://github.com/google/flax/blob/87a211135c6a377c8f29048a1cac3840e38b9da4/examples/wmt/train.py#L104
+        """
+        vocab_size = logits.shape[-1]
+        confidence = 1.0 - label_smoothing_factor
+        low_confidence = (1.0 - confidence) / (vocab_size - 1)
+        normalizing_constant = -(
+            confidence * jnp.log(confidence) + (vocab_size - 1) * low_confidence * jnp.log(low_confidence + 1e-20)
+        )
+        soft_labels = onehot(labels, vocab_size, on_value=confidence, off_value=low_confidence)
+
+        loss = optax.softmax_cross_entropy(logits, soft_labels)
+        loss = loss - normalizing_constant
+
+        # ignore padded tokens from loss, i.e. where labels are not set to -100
+        padding_mask = labels >= 0
+        loss = loss * padding_mask
+        loss = loss.sum()
+        num_labels = padding_mask.sum()
+        return loss, num_labels
+
+    # Define gradient update step fn
+    def train_step(state, batch, label_smoothing_factor=0.0):
+        dropout_rng, new_dropout_rng = jax.random.split(state.dropout_rng)
+
+        def compute_loss(params):
+            labels = batch.pop("labels")
+            logits = state.apply_fn(**batch, params=params, dropout_rng=dropout_rng, train=True)[0]
+            loss, num_labels = loss_fn(logits, labels, label_smoothing_factor)
+            return loss, num_labels
+
+        grad_fn = jax.value_and_grad(compute_loss, has_aux=True)
+        (loss, num_labels), grad = grad_fn(state.params)
+        num_labels = jax.lax.psum(num_labels, "batch")
+
+        # true loss = total loss / total samples
+        loss = jax.lax.psum(loss, "batch")
+        loss = jax.tree_util.tree_map(lambda x: x / num_labels, loss)
+
+        # true grad = total grad / total samples
+        grad = jax.lax.psum(grad, "batch")
+        grad = jax.tree_util.tree_map(lambda x: x / num_labels, grad)
+        new_state = state.apply_gradients(grads=grad, dropout_rng=new_dropout_rng)
+
+        metrics = {"loss": loss, "learning_rate": linear_decay_lr_schedule_fn(state.step)}
+        return new_state, metrics
+
+    # Define eval fn
+    def eval_step(params, batch, label_smoothing_factor=0.0):
+        labels = batch.pop("labels")
+        logits = model(**batch, params=params, train=False)[0]
+
+        loss, num_labels = loss_fn(logits, labels, label_smoothing_factor)
+        num_labels = jax.lax.psum(num_labels, "batch")
+
+        # true loss = total loss / total samples
+        loss = jax.lax.psum(loss, "batch")
+        loss = jax.tree_util.tree_map(lambda x: x / num_labels, loss)
+
+        metrics = {"loss": loss}
+        return metrics
+
+    # Define generation function
+    num_beams = model_args.num_beams if model_args.num_beams is not None else model.config.num_beams
+    gen_kwargs = {"max_length": max_label_length, "num_beams": num_beams}
+
+    def generate_step(params, batch):
+        model.params = params
+        output_ids = model.generate(batch[model_input_name], attention_mask=batch.get("attention_mask"), **gen_kwargs)
+        return output_ids.sequences
+
+    # Create parallel version of the train and eval step
+    p_train_step = jax.pmap(
+        partial(train_step, label_smoothing_factor=training_args.label_smoothing_factor), "batch", donate_argnums=(0,)
+    )
+    p_eval_step = jax.pmap(partial(eval_step, label_smoothing_factor=training_args.label_smoothing_factor), "batch")
+    p_generate_step = jax.pmap(generate_step, "batch")
+
+    # Replicate the train state on each device
+    state = state.replicate()
+
+    logger.info("***** Running training *****")
+    logger.info(f"  Num examples = {len(vectorized_datasets['train'])}")
+    logger.info(f"  Num Epochs = {num_epochs}")
+    logger.info(f"  Instantaneous batch size per device = {training_args.per_device_train_batch_size}")
+    logger.info(f"  Total train batch size (w. parallel & distributed) = {train_batch_size}")
+    logger.info(f"  Total optimization steps = {total_train_steps}")
+
+    train_time = 0
+    epochs = tqdm(range(num_epochs), desc=f"Epoch ... (1/{num_epochs})", position=0)
+    for epoch in epochs:
+        # ======================== Training ================================
+        train_start = time.time()
+
+        train_metrics = []
+
+        # Generate an epoch by shuffling sampling indices from the train dataset and create a data loader
+        vectorized_datasets["train"] = vectorized_datasets["train"].shuffle(training_args.seed)
+        train_loader = DataLoader(
+            vectorized_datasets["train"],
+            batch_size=train_batch_size,
+            drop_last=True,
+            collate_fn=data_collator,
+            num_workers=training_args.dataloader_num_workers,
+        )
+        # train
+        for batch in tqdm(train_loader, desc="Training...", position=1, leave=False):
+            batch = shard(batch.data)
+            state, train_metric = p_train_step(state, batch)
+            train_metrics.append(train_metric)
+
+        train_time += time.time() - train_start
+
+        train_metric = unreplicate(train_metric)
+
+        epochs.write(
+            f"Epoch... ({epoch + 1}/{num_epochs} | Loss: {train_metric['loss']}, Learning Rate:"
+            f" {train_metric['learning_rate']})"
+        )
+
+        # ======================== Evaluating ==============================
+        eval_metrics = []
+        eval_preds = []
+        eval_labels = []
+
+        eval_loader = DataLoader(
+            vectorized_datasets["eval"],
+            batch_size=eval_batch_size,
+            drop_last=False,
+            collate_fn=data_collator,
+            num_workers=training_args.dataloader_num_workers,
+        )
+        for batch in tqdm(eval_loader, desc="Evaluating...", position=2, leave=False):
+            # Model forward
+            labels = batch["labels"]
+
+            metrics = pad_shard_unpad(p_eval_step, static_return=True)(
+                state.params, batch.data, min_device_batch=per_device_eval_batch_size
+            )
+            eval_metrics.append(metrics)
+
+            # generation
+            if training_args.predict_with_generate:
+                generated_ids = pad_shard_unpad(p_generate_step)(state.params, batch.data)
+                eval_preds.extend(jax.device_get(generated_ids.reshape(-1, gen_kwargs["max_length"])))
+                eval_labels.extend(labels)
+
+        # normalize eval metrics
+        eval_metrics = get_metrics(eval_metrics)
+        eval_metrics = jax.tree_util.tree_map(jnp.mean, eval_metrics)
+
+        # compute WER metric
+        wer_desc = ""
+        if training_args.predict_with_generate:
+            wer_metric = compute_metrics(eval_preds, eval_labels)
+            eval_metrics.update(wer_metric)
+            wer_desc = " ".join([f"Eval {key}: {value} |" for key, value in wer_metric.items()])
+
+        # Print metrics and update progress bar
+        desc = f"Epoch... ({epoch + 1}/{num_epochs} | Eval Loss: {eval_metrics['loss']} | {wer_desc})"
+        epochs.write(desc)
+        epochs.desc = desc
+
+        # Save metrics
+        if has_tensorboard and jax.process_index() == 0:
+            cur_step = epoch * (len(vectorized_datasets["train"]) // train_batch_size)
+            write_metric(summary_writer, train_metrics, eval_metrics, train_time, cur_step)
+
+        # save checkpoint after each epoch and push checkpoint to the hub
+        if jax.process_index() == 0:
+            params = jax.device_get(jax.tree_util.tree_map(lambda x: x[0], state.params))
+            model.save_pretrained(training_args.output_dir, params=params)
+            tokenizer.save_pretrained(training_args.output_dir)
+            if training_args.push_to_hub:
+                repo.push_to_hub(commit_message=f"Saving weights and logs of epoch {epoch}", blocking=False)
+
+
+if __name__ == "__main__":
+    main()

examples/flax/test_flax_examples.py

@@ -32,6 +32,7 @@ SRC_DIRS = [
         "summarization",
         "token-classification",
         "question-answering",
+        "speech-recognition",
     ]
 ]
 sys.path.extend(SRC_DIRS)
@@ -41,6 +42,7 @@ if SRC_DIRS is not None:
     import run_clm_flax
     import run_flax_glue
     import run_flax_ner
+    import run_flax_speech_recognition_seq2seq
     import run_mlm_flax
     import run_qa
     import run_summarization_flax
@@ -252,3 +254,32 @@ class ExamplesTests(TestCasePlus):
             result = get_results(tmp_dir)
             self.assertGreaterEqual(result["eval_f1"], 30)
             self.assertGreaterEqual(result["eval_exact"], 30)
+
+    @slow
+    def test_run_flax_speech_recognition_seq2seq(self):
+        tmp_dir = self.get_auto_remove_tmp_dir()
+        testargs = f"""
+            run_flax_speech_recognition_seq2seq.py
+            --model_name_or_path openai/whisper-tiny.en
+            --dataset_name hf-internal-testing/librispeech_asr_dummy
+            --dataset_config clean
+            --train_split_name validation
+            --eval_split_name validation
+            --output_dir {tmp_dir}
+            --overwrite_output_dir
+            --num_train_epochs=2
+            --max_train_samples 10
+            --max_eval_samples 10
+            --warmup_steps=8
+            --do_train
+            --do_eval
+            --learning_rate=2e-4
+            --per_device_train_batch_size=2
+            --per_device_eval_batch_size=1
+            --predict_with_generate
+        """.split()
+
+        with patch.object(sys, "argv", testargs):
+            run_flax_speech_recognition_seq2seq.main()
+            result = get_results(tmp_dir, split="eval")
+            self.assertLessEqual(result["eval_wer"], 0.05)