whole.py

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# %% [markdown] id="SX7UC-8jTsp7" tags=[]
#
# <center><h1>The Annotated Transformer</h1> </center>
#
#
# <center>
# <p><a href="https://arxiv.org/abs/1706.03762">Attention is All You Need
# </a></p>
# </center>
#
# <img src="images/aiayn.png" width="70%"/>
#
# * *v2022: Austin Huang, Suraj Subramanian, Jonathan Sum, Khalid Almubarak,
#    and Stella Biderman.*
# * *[Original](https://nlp.seas.harvard.edu/2018/04/03/attention.html):
#    [Sasha Rush](http://rush-nlp.com/).*
#
#
# The Transformer has been on a lot of
# people's minds over the last <s>year</s> five years.
# This post presents an annotated version of the paper in the
# form of a line-by-line implementation. It reorders and deletes
# some sections from the original paper and adds comments
# throughout. This document itself is a working notebook, and should
# be a completely usable implementation.
# Code is available
# [here](https://github.com/harvardnlp/annotated-transformer/).
#


# %% [markdown] id="RSntDwKhTsp-"
# <h3> Table of Contents </h3>
# <ul>
# <li><a href="#prelims">Prelims</a></li>
# <li><a href="#background">Background</a></li>
# <li><a href="#part-1-model-architecture">Part 1: Model Architecture</a></li>
# <li><a href="#model-architecture">Model Architecture</a><ul>
# <li><a href="#encoder-and-decoder-stacks">Encoder and Decoder Stacks</a></li>
# <li><a href="#position-wise-feed-forward-networks">Position-wise Feed-Forward
# Networks</a></li>
# <li><a href="#embeddings-and-softmax">Embeddings and Softmax</a></li>
# <li><a href="#positional-encoding">Positional Encoding</a></li>
# <li><a href="#full-model">Full Model</a></li>
# <li><a href="#inference">Inference:</a></li>
# </ul></li>
# <li><a href="#part-2-model-training">Part 2: Model Training</a></li>
# <li><a href="#training">Training</a><ul>
# <li><a href="#batches-and-masking">Batches and Masking</a></li>
# <li><a href="#training-loop">Training Loop</a></li>
# <li><a href="#training-data-and-batching">Training Data and Batching</a></li>
# <li><a href="#hardware-and-schedule">Hardware and Schedule</a></li>
# <li><a href="#optimizer">Optimizer</a></li>
# <li><a href="#regularization">Regularization</a></li>
# </ul></li>
# <li><a href="#a-first-example">A First Example</a><ul>
# <li><a href="#synthetic-data">Synthetic Data</a></li>
# <li><a href="#loss-computation">Loss Computation</a></li>
# <li><a href="#greedy-decoding">Greedy Decoding</a></li>
# </ul></li>
# <li><a href="#part-3-a-real-world-example">Part 3: A Real World Example</a>
# <ul>
# <li><a href="#data-loading">Data Loading</a></li>
# <li><a href="#iterators">Iterators</a></li>
# <li><a href="#training-the-system">Training the System</a></li>
# </ul></li>
# <li><a href="#additional-components-bpe-search-averaging">Additional
# Components: BPE, Search, Averaging</a></li>
# <li><a href="#results">Results</a><ul>
# <li><a href="#attention-visualization">Attention Visualization</a></li>
# <li><a href="#encoder-self-attention">Encoder Self Attention</a></li>
# <li><a href="#decoder-self-attention">Decoder Self Attention</a></li>
# <li><a href="#decoder-src-attention">Decoder Src Attention</a></li>
# </ul></li>
# <li><a href="#conclusion">Conclusion</a></li>
# </ul>


# %% [markdown] id="BhmOhn9lTsp8"
# # Prelims
#
# <a href="#background">Skip</a>

# %% id="NwClcbH6Tsp8"
# # !pip install -r requirements.txt

# %% id="NwClcbH6Tsp8"
# # Uncomment for colab
# #
# # !pip install -q torchdata==0.3.0 torchtext==0.12 spacy==3.2 altair GPUtil
# # !python -m spacy download de_core_news_sm
# # !python -m spacy download en_core_web_sm


# %% id="v1-1MX6oTsp9"
import os
from os.path import exists
import torch
import torch.nn as nn
from torch.nn.functional import log_softmax, pad
import math
import copy
import time
from torch.optim.lr_scheduler import LambdaLR
import pandas as pd
import altair as alt
# from torchtext.data.functional import to_map_style_dataset
# from torch.utils.data import DataLoader
# from torchtext.vocab import build_vocab_from_iterator
# import torchtext.datasets as datasets
# import spacy
# import GPUtil
import warnings
from torch.utils.data.distributed import DistributedSampler
import torch.distributed as dist
import torch.multiprocessing as mp
from torch.nn.parallel import DistributedDataParallel as DDP


# Set to False to skip notebook execution (e.g. for debugging)
warnings.filterwarnings("ignore")
RUN_EXAMPLES = True


# %%
# Some convenience helper functions used throughout the notebook


def is_interactive_notebook():
    return __name__ == "__main__"


def show_example(fn, args=[]):
    if __name__ == "__main__" and RUN_EXAMPLES:
        return fn(*args)


def execute_example(fn, args=[]):
    if __name__ == "__main__" and RUN_EXAMPLES:
        fn(*args)


class DummyOptimizer(torch.optim.Optimizer):
    def __init__(self):
        self.param_groups = [{"lr": 0}]
        None

    def step(self):
        None

    def zero_grad(self, set_to_none=False):
        None


class DummyScheduler:
    def step(self):
        None


# %% [markdown] id="jx49WRyfTsp-"
# > My comments are blockquoted. The main text is all from the paper itself.

# %% [markdown] id="7phVeWghTsp_"
# # Background

# %% [markdown] id="83ZDS91dTsqA"
#
# The goal of reducing sequential computation also forms the
# foundation of the Extended Neural GPU, ByteNet and ConvS2S, all of
# which use convolutional neural networks as basic building block,
# computing hidden representations in parallel for all input and
# output positions. In these models, the number of operations required
# to relate signals from two arbitrary input or output positions grows
# in the distance between positions, linearly for ConvS2S and
# logarithmically for ByteNet. This makes it more difficult to learn
# dependencies between distant positions. In the Transformer this is
# reduced to a constant number of operations, albeit at the cost of
# reduced effective resolution due to averaging attention-weighted
# positions, an effect we counteract with Multi-Head Attention.
#
# Self-attention, sometimes called intra-attention is an attention
# mechanism relating different positions of a single sequence in order
# to compute a representation of the sequence. Self-attention has been
# used successfully in a variety of tasks including reading
# comprehension, abstractive summarization, textual entailment and
# learning task-independent sentence representations. End-to-end
# memory networks are based on a recurrent attention mechanism instead
# of sequencealigned recurrence and have been shown to perform well on
# simple-language question answering and language modeling tasks.
#
# To the best of our knowledge, however, the Transformer is the first
# transduction model relying entirely on self-attention to compute
# representations of its input and output without using sequence
# aligned RNNs or convolution.

# %% [markdown]
# # Part 1: Model Architecture

# %% [markdown] id="pFrPajezTsqB"
# # Model Architecture

# %% [markdown] id="ReuU_h-fTsqB"
#
# Most competitive neural sequence transduction models have an
# encoder-decoder structure
# [(cite)](https://arxiv.org/abs/1409.0473). Here, the encoder maps an
# input sequence of symbol representations $(x_1, ..., x_n)$ to a
# sequence of continuous representations $\mathbf{z} = (z_1, ...,
# z_n)$. Given $\mathbf{z}$, the decoder then generates an output
# sequence $(y_1,...,y_m)$ of symbols one element at a time. At each
# step the model is auto-regressive
# [(cite)](https://arxiv.org/abs/1308.0850), consuming the previously
# generated symbols as additional input when generating the next.

# %% id="k0XGXhzRTsqB"
class EncoderDecoder(nn.Module):
    """
    A standard Encoder-Decoder architecture. Base for this and many
    other models.
    """

    def __init__(self, encoder, decoder, src_embed, tgt_embed, generator):
        super(EncoderDecoder, self).__init__()
        self.encoder = encoder
        self.decoder = decoder
        self.src_embed = src_embed
        self.tgt_embed = tgt_embed
        self.generator = generator

    def forward(self, src, tgt, src_mask, tgt_mask):
        "Take in and process masked src and target sequences."
        return self.decode(self.encode(src, src_mask), src_mask, tgt, tgt_mask)

    def encode(self, src, src_mask):
        return self.encoder(self.src_embed(src), src_mask)

    def decode(self, memory, src_mask, tgt, tgt_mask):
        return self.decoder(self.tgt_embed(tgt), memory, src_mask, tgt_mask)


# %% id="NKGoH2RsTsqC"
class Generator(nn.Module):
    "Define standard linear + softmax generation step."

    def __init__(self, d_model, vocab):
        super(Generator, self).__init__()
        self.proj = nn.Linear(d_model, vocab)

    def forward(self, x):
        return log_softmax(self.proj(x), dim=-1)


# %% [markdown] id="mOoEnF_jTsqC"
#
# The Transformer follows this overall architecture using stacked
# self-attention and point-wise, fully connected layers for both the
# encoder and decoder, shown in the left and right halves of Figure 1,
# respectively.

# %% [markdown] id="oredWloYTsqC"
# ![](images/ModalNet-21.png)


# %% [markdown] id="bh092NZBTsqD"
# ## Encoder and Decoder Stacks
#
# ### Encoder
#
# The encoder is composed of a stack of $N=6$ identical layers.

# %% id="2gxTApUYTsqD"
def clones(module, N):
    "Produce N identical layers."
    return nn.ModuleList([copy.deepcopy(module) for _ in range(N)])


# %% id="xqVTz9MkTsqD"
class Encoder(nn.Module):
    "Core encoder is a stack of N layers"

    def __init__(self, layer, N):
        super(Encoder, self).__init__()
        self.layers = clones(layer, N)
        self.norm = LayerNorm(layer.size)

    def forward(self, x, mask):
        "Pass the input (and mask) through each layer in turn."
        #print(mask.size())
        for layer in self.layers:
            x = layer(x, mask)
        return self.norm(x)


# %% [markdown] id="GjAKgjGwTsqD"
#
# We employ a residual connection
# [(cite)](https://arxiv.org/abs/1512.03385) around each of the two
# sub-layers, followed by layer normalization
# [(cite)](https://arxiv.org/abs/1607.06450).

# %% id="3jKa_prZTsqE"
class LayerNorm(nn.Module):
    "Construct a layernorm module (See citation for details)."

    def __init__(self, features, eps=1e-6):
        super(LayerNorm, self).__init__()
        self.a_2 = nn.Parameter(torch.ones(features))
        self.b_2 = nn.Parameter(torch.zeros(features))
        self.eps = eps

    def forward(self, x):
        mean = x.mean(-1, keepdim=True)
        std = x.std(-1, keepdim=True)
        return self.a_2 * (x - mean) / (std + self.eps) + self.b_2


# %% [markdown] id="nXSJ3QYmTsqE"
#
# That is, the output of each sub-layer is $\mathrm{LayerNorm}(x +
# \mathrm{Sublayer}(x))$, where $\mathrm{Sublayer}(x)$ is the function
# implemented by the sub-layer itself.  We apply dropout
# [(cite)](http://jmlr.org/papers/v15/srivastava14a.html) to the
# output of each sub-layer, before it is added to the sub-layer input
# and normalized.
#
# To facilitate these residual connections, all sub-layers in the
# model, as well as the embedding layers, produce outputs of dimension
# $d_{\text{model}}=512$.

# %% id="U1P7zI0eTsqE"
class SublayerConnection(nn.Module):
    """
    A residual connection followed by a layer norm.
    Note for code simplicity the norm is first as opposed to last.
    """

    def __init__(self, size, dropout):
        super(SublayerConnection, self).__init__()
        self.norm = LayerNorm(size)
        self.dropout = nn.Dropout(dropout)

    def forward(self, x, sublayer):
        "Apply residual connection to any sublayer with the same size."
        return x + self.dropout(sublayer(self.norm(x)))


# %% [markdown] id="ML6oDlEqTsqE"
#
# Each layer has two sub-layers. The first is a multi-head
# self-attention mechanism, and the second is a simple, position-wise
# fully connected feed-forward network.

# %% id="qYkUFr6GTsqE"
class EncoderLayer(nn.Module):
    "Encoder is made up of self-attn and feed forward (defined below)"

    def __init__(self, size, self_attn, feed_forward, dropout):
        super(EncoderLayer, self).__init__()
        self.self_attn = self_attn
        self.feed_forward = feed_forward
        self.sublayer = clones(SublayerConnection(size, dropout), 2)
        self.size = size

    def forward(self, x, mask):
        "Follow Figure 1 (left) for connections."
        x = self.sublayer[0](x, lambda x: self.self_attn(x, x, x, mask))
        return self.sublayer[1](x, self.feed_forward)


# %% [markdown] id="7ecOQIhkTsqF"
# ### Decoder
#
# The decoder is also composed of a stack of $N=6$ identical layers.
#

# %%
class Decoder(nn.Module):
    "Generic N layer decoder with masking."

    def __init__(self, layer, N):
        super(Decoder, self).__init__()
        self.layers = clones(layer, N)
        self.norm = LayerNorm(layer.size)

    def forward(self, x, memory, src_mask, tgt_mask):
        for layer in self.layers:
            x = layer(x, memory, src_mask, tgt_mask)
        return self.norm(x)


# %% [markdown] id="dXlCB12pTsqF"
#
# In addition to the two sub-layers in each encoder layer, the decoder
# inserts a third sub-layer, which performs multi-head attention over
# the output of the encoder stack.  Similar to the encoder, we employ
# residual connections around each of the sub-layers, followed by
# layer normalization.

# %% id="M2hA1xFQTsqF"
class DecoderLayer(nn.Module):
    "Decoder is made of self-attn, src-attn, and feed forward (defined below)"

    def __init__(self, size, self_attn, src_attn, feed_forward, dropout):
        super(DecoderLayer, self).__init__()
        self.size = size
        self.self_attn = self_attn
        self.src_attn = src_attn
        self.feed_forward = feed_forward
        self.sublayer = clones(SublayerConnection(size, dropout), 3)

    def forward(self, x, memory, src_mask, tgt_mask):
        "Follow Figure 1 (right) for connections."
        m = memory
        x = self.sublayer[0](x, lambda x: self.self_attn(x, x, x, tgt_mask))
        x = self.sublayer[1](x, lambda x: self.src_attn(x, m, m, src_mask))
        return self.sublayer[2](x, self.feed_forward)


# %% [markdown] id="FZz5rLl4TsqF"
#
# We also modify the self-attention sub-layer in the decoder stack to
# prevent positions from attending to subsequent positions.  This
# masking, combined with fact that the output embeddings are offset by
# one position, ensures that the predictions for position $i$ can
# depend only on the known outputs at positions less than $i$.

# %% id="QN98O2l3TsqF"
def subsequent_mask(size):
    "Mask out subsequent positions."
    attn_shape = (1, size, size)
    subsequent_mask = torch.triu(torch.ones(attn_shape), diagonal=1).type(
        torch.uint8
    )
    return subsequent_mask == 0


# %% [markdown] id="Vg_f_w-PTsqG"
#
# > Below the attention mask shows the position each tgt word (row) is
# > allowed to look at (column). Words are blocked for attending to
# > future words during training.

# %% id="ht_FtgYAokC4"
def example_mask():
    LS_data = pd.concat(
        [
            pd.DataFrame(
                {
                    "Subsequent Mask": subsequent_mask(20)[0][x, y].flatten(),
                    "Window": y,
                    "Masking": x,
                }
            )
            for y in range(20)
            for x in range(20)
        ]
    )

    return (
        alt.Chart(LS_data)
        .mark_rect()
        .properties(height=250, width=250)
        .encode(
            alt.X("Window:O"),
            alt.Y("Masking:O"),
            alt.Color("Subsequent Mask:Q", scale=alt.Scale(scheme="viridis")),
        )
        .interactive()
    )


show_example(example_mask)

# %% [markdown] id="Qto_yg7BTsqG"
# ### Attention
#
# An attention function can be described as mapping a query and a set
# of key-value pairs to an output, where the query, keys, values, and
# output are all vectors.  The output is computed as a weighted sum of
# the values, where the weight assigned to each value is computed by a
# compatibility function of the query with the corresponding key.
#
# We call our particular attention "Scaled Dot-Product Attention".
# The input consists of queries and keys of dimension $d_k$, and
# values of dimension $d_v$.  We compute the dot products of the query
# with all keys, divide each by $\sqrt{d_k}$, and apply a softmax
# function to obtain the weights on the values.
#
#
#
# ![](images/ModalNet-19.png)


# %% [markdown] id="EYJLWk6cTsqG"
#
# In practice, we compute the attention function on a set of queries
# simultaneously, packed together into a matrix $Q$.  The keys and
# values are also packed together into matrices $K$ and $V$.  We
# compute the matrix of outputs as:
#
# $$
#    \mathrm{Attention}(Q, K, V) = \mathrm{softmax}(\frac{QK^T}{\sqrt{d_k}})V
# $$

# %% id="qsoVxS5yTsqG"
def attention(query, key, value, mask=None, dropout=None):
    "Compute 'Scaled Dot Product Attention'"
    d_k = query.size(-1)
    scores = torch.matmul(query, key.transpose(-2, -1)) / math.sqrt(d_k)
    if mask is not None:
        scores = scores.masked_fill(mask == 0, -1e9)
    p_attn = scores.softmax(dim=-1)
    if dropout is not None:
        p_attn = dropout(p_attn)
    return torch.matmul(p_attn, value), p_attn


# %% [markdown] id="jUkpwu8kTsqG"
#
# The two most commonly used attention functions are additive
# attention [(cite)](https://arxiv.org/abs/1409.0473), and dot-product
# (multiplicative) attention.  Dot-product attention is identical to
# our algorithm, except for the scaling factor of
# $\frac{1}{\sqrt{d_k}}$. Additive attention computes the
# compatibility function using a feed-forward network with a single
# hidden layer.  While the two are similar in theoretical complexity,
# dot-product attention is much faster and more space-efficient in
# practice, since it can be implemented using highly optimized matrix
# multiplication code.
#
#
# While for small values of $d_k$ the two mechanisms perform
# similarly, additive attention outperforms dot product attention
# without scaling for larger values of $d_k$
# [(cite)](https://arxiv.org/abs/1703.03906). We suspect that for
# large values of $d_k$, the dot products grow large in magnitude,
# pushing the softmax function into regions where it has extremely
# small gradients (To illustrate why the dot products get large,
# assume that the components of $q$ and $k$ are independent random
# variables with mean $0$ and variance $1$.  Then their dot product,
# $q \cdot k = \sum_{i=1}^{d_k} q_ik_i$, has mean $0$ and variance
# $d_k$.). To counteract this effect, we scale the dot products by
# $\frac{1}{\sqrt{d_k}}$.
#
#

# %% [markdown] id="bS1FszhVTsqG"
# ![](images/ModalNet-20.png)


# %% [markdown] id="TNtVyZ-pTsqH"
#
# Multi-head attention allows the model to jointly attend to
# information from different representation subspaces at different
# positions. With a single attention head, averaging inhibits this.
#
# $$
# \mathrm{MultiHead}(Q, K, V) =
#     \mathrm{Concat}(\mathrm{head_1}, ..., \mathrm{head_h})W^O \\
#     \text{where}~\mathrm{head_i} = \mathrm{Attention}(QW^Q_i, KW^K_i, VW^V_i)
# $$
#
# Where the projections are parameter matrices $W^Q_i \in
# \mathbb{R}^{d_{\text{model}} \times d_k}$, $W^K_i \in
# \mathbb{R}^{d_{\text{model}} \times d_k}$, $W^V_i \in
# \mathbb{R}^{d_{\text{model}} \times d_v}$ and $W^O \in
# \mathbb{R}^{hd_v \times d_{\text{model}}}$.
#
# In this work we employ $h=8$ parallel attention layers, or
# heads. For each of these we use $d_k=d_v=d_{\text{model}}/h=64$. Due
# to the reduced dimension of each head, the total computational cost
# is similar to that of single-head attention with full
# dimensionality.

# %% id="D2LBMKCQTsqH"
class MultiHeadedAttention(nn.Module):
    def __init__(self, h, d_model, dropout=0.1):
        "Take in model size and number of heads."
        super(MultiHeadedAttention, self).__init__()
        assert d_model % h == 0
        # We assume d_v always equals d_k
        self.d_k = d_model // h
        self.h = h
        self.linears = clones(nn.Linear(d_model, d_model), 4)
        self.attn = None
        self.dropout = nn.Dropout(p=dropout)

    def forward(self, query, key, value, mask=None):
        "Implements Figure 2"
        if mask is not None:
            # Same mask applied to all h heads.
            mask = mask.unsqueeze(1)
        nbatches = query.size(0)

        # 1) Do all the linear projections in batch from d_model => h x d_k
        query, key, value = [
            lin(x).view(nbatches, -1, self.h, self.d_k).transpose(1, 2)
            for lin, x in zip(self.linears, (query, key, value))
        ]
        #print(mask.size())
        # 2) Apply attention on all the projected vectors in batch.
        x, self.attn = attention(
            query, key, value, mask=mask, dropout=self.dropout
        )

        # 3) "Concat" using a view and apply a final linear.
        x = (
            x.transpose(1, 2)
            .contiguous()
            .view(nbatches, -1, self.h * self.d_k)
        )
        del query
        del key
        del value
        return self.linears[-1](x)


# %% [markdown] id="EDRba3J3TsqH"
# ### Applications of Attention in our Model
#
# The Transformer uses multi-head attention in three different ways:
# 1) In "encoder-decoder attention" layers, the queries come from the
# previous decoder layer, and the memory keys and values come from the
# output of the encoder.  This allows every position in the decoder to
# attend over all positions in the input sequence.  This mimics the
# typical encoder-decoder attention mechanisms in sequence-to-sequence
# models such as [(cite)](https://arxiv.org/abs/1609.08144).
#
#
# 2) The encoder contains self-attention layers.  In a self-attention
# layer all of the keys, values and queries come from the same place,
# in this case, the output of the previous layer in the encoder.  Each
# position in the encoder can attend to all positions in the previous
# layer of the encoder.
#
#
# 3) Similarly, self-attention layers in the decoder allow each
# position in the decoder to attend to all positions in the decoder up
# to and including that position.  We need to prevent leftward
# information flow in the decoder to preserve the auto-regressive
# property.  We implement this inside of scaled dot-product attention
# by masking out (setting to $-\infty$) all values in the input of the
# softmax which correspond to illegal connections.

# %% [markdown] id="M-en97_GTsqH"
# ## Position-wise Feed-Forward Networks
#
# In addition to attention sub-layers, each of the layers in our
# encoder and decoder contains a fully connected feed-forward network,
# which is applied to each position separately and identically.  This
# consists of two linear transformations with a ReLU activation in
# between.
#
# $$\mathrm{FFN}(x)=\max(0, xW_1 + b_1) W_2 + b_2$$
#
# While the linear transformations are the same across different
# positions, they use different parameters from layer to
# layer. Another way of describing this is as two convolutions with
# kernel size 1.  The dimensionality of input and output is
# $d_{\text{model}}=512$, and the inner-layer has dimensionality
# $d_{ff}=2048$.

# %% id="6HHCemCxTsqH"
class PositionwiseFeedForward(nn.Module):
    "Implements FFN equation."

    def __init__(self, d_model, d_ff, dropout=0.1):
        super(PositionwiseFeedForward, self).__init__()
        self.w_1 = nn.Linear(d_model, d_ff)
        self.w_2 = nn.Linear(d_ff, d_model)
        self.dropout = nn.Dropout(dropout)

    def forward(self, x):
        return self.w_2(self.dropout(self.w_1(x).relu()))


# %% [markdown] id="dR1YM520TsqH"
# ## Embeddings and Softmax
#
# Similarly to other sequence transduction models, we use learned
# embeddings to convert the input tokens and output tokens to vectors
# of dimension $d_{\text{model}}$.  We also use the usual learned
# linear transformation and softmax function to convert the decoder
# output to predicted next-token probabilities.  In our model, we
# share the same weight matrix between the two embedding layers and
# the pre-softmax linear transformation, similar to
# [(cite)](https://arxiv.org/abs/1608.05859). In the embedding layers,
# we multiply those weights by $\sqrt{d_{\text{model}}}$.

# %% id="pyrChq9qTsqH"
class Embeddings(nn.Module):
    def __init__(self, d_model, vocab):
        super(Embeddings, self).__init__()
        self.lut = nn.Embedding(vocab, d_model)
        self.d_model = d_model

    def forward(self, x):
        return self.lut(x) * math.sqrt(self.d_model)


# %% [markdown] id="vOkdui-cTsqH"
# ## Positional Encoding
#
# Since our model contains no recurrence and no convolution, in order
# for the model to make use of the order of the sequence, we must
# inject some information about the relative or absolute position of
# the tokens in the sequence.  To this end, we add "positional
# encodings" to the input embeddings at the bottoms of the encoder and
# decoder stacks.  The positional encodings have the same dimension
# $d_{\text{model}}$ as the embeddings, so that the two can be summed.
# There are many choices of positional encodings, learned and fixed
# [(cite)](https://arxiv.org/pdf/1705.03122.pdf).
#
# In this work, we use sine and cosine functions of different frequencies:
#
# $$PE_{(pos,2i)} = \sin(pos / 10000^{2i/d_{\text{model}}})$$
#
# $$PE_{(pos,2i+1)} = \cos(pos / 10000^{2i/d_{\text{model}}})$$
#
# where $pos$ is the position and $i$ is the dimension.  That is, each
# dimension of the positional encoding corresponds to a sinusoid.  The
# wavelengths form a geometric progression from $2\pi$ to $10000 \cdot
# 2\pi$.  We chose this function because we hypothesized it would
# allow the model to easily learn to attend by relative positions,
# since for any fixed offset $k$, $PE_{pos+k}$ can be represented as a
# linear function of $PE_{pos}$.
#
# In addition, we apply dropout to the sums of the embeddings and the
# positional encodings in both the encoder and decoder stacks.  For
# the base model, we use a rate of $P_{drop}=0.1$.
#
#

# %% id="zaHGD4yJTsqH"
class PositionalEncoding(nn.Module):
    "Implement the PE function."

    def __init__(self, d_model, dropout, max_len=5000):
        super(PositionalEncoding, self).__init__()
        self.dropout = nn.Dropout(p=dropout)

        # Compute the positional encodings once in log space.
        pe = torch.zeros(max_len, d_model)
        position = torch.arange(0, max_len).unsqueeze(1)
        div_term = torch.exp(
            torch.arange(0, d_model, 2) * -(math.log(10000.0) / d_model)
        )
        pe[:, 0::2] = torch.sin(position * div_term)
        pe[:, 1::2] = torch.cos(position * div_term)
        pe = pe.unsqueeze(0)
        self.register_buffer("pe", pe)

    def forward(self, x):
        x = x + self.pe[:, : x.size(1)].requires_grad_(False)
        return self.dropout(x)


# %% [markdown] id="EfHacTJLTsqH"
#
# > Below the positional encoding will add in a sine wave based on
# > position. The frequency and offset of the wave is different for
# > each dimension.

# %% id="rnvHk_1QokC6" type="example"
def example_positional():
    pe = PositionalEncoding(20, 0)
    y = pe.forward(torch.zeros(1, 100, 20))

    data = pd.concat(
        [
            pd.DataFrame(
                {
                    "embedding": y[0, :, dim],
                    "dimension": dim,
                    "position": list(range(100)),
                }
            )
            for dim in [4, 5, 6, 7]
        ]
    )

    return (
        alt.Chart(data)
        .mark_line()
        .properties(width=800)
        .encode(x="position", y="embedding", color="dimension:N")
        .interactive()
    )


#show_example(example_positional)


# %% [markdown] id="g8rZNCrzTsqI"
#
# We also experimented with using learned positional embeddings
# [(cite)](https://arxiv.org/pdf/1705.03122.pdf) instead, and found
# that the two versions produced nearly identical results.  We chose
# the sinusoidal version because it may allow the model to extrapolate
# to sequence lengths longer than the ones encountered during
# training.

# %% [markdown] id="iwNKCzlyTsqI"
# ## Full Model
#
# > Here we define a function from hyperparameters to a full model.

# %% id="mPe1ES0UTsqI"
def make_model(
    src_vocab, tgt_vocab, N=6, d_model=512, d_ff=2048, h=8, dropout=0.1
):
    "Helper: Construct a model from hyperparameters."
    c = copy.deepcopy
    attn = MultiHeadedAttention(h, d_model)
    ff = PositionwiseFeedForward(d_model, d_ff, dropout)
    position = PositionalEncoding(d_model, dropout)
    model = EncoderDecoder(
        Encoder(EncoderLayer(d_model, c(attn), c(ff), dropout), N),
        Decoder(DecoderLayer(d_model, c(attn), c(attn), c(ff), dropout), N),
        nn.Sequential(Embeddings(d_model, src_vocab), c(position)),
        nn.Sequential(Embeddings(d_model, tgt_vocab), c(position)),
        Generator(d_model, tgt_vocab),
    )

    # This was important from their code.
    # Initialize parameters with Glorot / fan_avg.
    for p in model.parameters():
        if p.dim() > 1:
            nn.init.xavier_uniform_(p)
    return model


# %% [markdown]
# ## Inference:
#
# > Here we make a forward step to generate a prediction of the
# model. We try to use our transformer to memorize the input. As you
# will see the output is randomly generated due to the fact that the
# model is not trained yet. In the next tutorial we will build the
# training function and try to train our model to memorize the numbers
# from 1 to 10.

# %%
def inference_test():
    test_model = make_model(11, 11, 2)
    test_model.eval()
    src = torch.LongTensor([[1, 2, 3, 4, 5, 6, 7, 8, 9, 10]])
    src_mask = torch.ones(1, 1, 10)

    memory = test_model.encode(src, src_mask)
    ys = torch.zeros(1, 1).type_as(src)

    for i in range(9):
        out = test_model.decode(
            memory, src_mask, ys, subsequent_mask(ys.size(1)).type_as(src.data)
        )
        prob = test_model.generator(out[:, -1])
        _, next_word = torch.max(prob, dim=1)
        next_word = next_word.data[0]
        ys = torch.cat(
            [ys, torch.empty(1, 1).type_as(src.data).fill_(next_word)], dim=1
        )

    print("Example Untrained Model Prediction:", ys)


def run_tests():
    for _ in range(10):
        inference_test()


#show_example(run_tests)


# %% [markdown]
# # Part 2: Model Training

# %% [markdown] id="05s6oT9fTsqI"
# # Training
#
# This section describes the training regime for our models.

# %% [markdown] id="fTxlofs4TsqI"
#
# > We stop for a quick interlude to introduce some of the tools
# > needed to train a standard encoder decoder model. First we define a
# > batch object that holds the src and target sentences for training,
# > as well as constructing the masks.

# %% [markdown] id="G7SkCenXTsqI"
# ## Batches and Masking

# %%
class Batch:
    """Object for holding a batch of data with mask during training."""

    def __init__(self, src, tgt=None, pad=2):  # 2 = <blank>
        self.src = src
        self.src_mask = (src != pad).unsqueeze(-2)
        if tgt is not None:
            self.tgt = tgt[:, :-1]
            self.tgt_y = tgt[:, 1:]
            self.tgt_mask = self.make_std_mask(self.tgt, pad)
            self.ntokens = (self.tgt_y != pad).data.sum()

    @staticmethod
    def make_std_mask(tgt, pad):
        "Create a mask to hide padding and future words."
        tgt_mask = (tgt != pad).unsqueeze(-2)
        tgt_mask = tgt_mask & subsequent_mask(tgt.size(-1)).type_as(
            tgt_mask.data
        )
        return tgt_mask


# %% [markdown] id="cKkw5GjLTsqI"
#
# > Next we create a generic training and scoring function to keep
# > track of loss. We pass in a generic loss compute function that
# > also handles parameter updates.

# %% [markdown] id="Q8zzeUc0TsqJ"
# ## Training Loop

# %%
class TrainState:
    """Track number of steps, examples, and tokens processed"""

    step: int = 0  # Steps in the current epoch
    accum_step: int = 0  # Number of gradient accumulation steps
    samples: int = 0  # total # of examples used
    tokens: int = 0  # total # of tokens processed


# %% id="2HAZD3hiTsqJ"
def run_epoch(
    data_iter,
    model,
    loss_compute,
    optimizer,
    scheduler,
    mode="train",
    accum_iter=1,
    train_state=TrainState(),
):
    """Train a single epoch"""
    start = time.time()
    total_tokens = 0
    total_loss = 0
    tokens = 0
    n_accum = 0
    for i, batch in enumerate(data_iter):
        #print(batch.src_mask.size(), batch.tgt_mask.size())
        out = model.forward(
            batch.src, batch.tgt, batch.src_mask, batch.tgt_mask
        )
        loss, loss_node = loss_compute(out, batch.tgt_y, batch.ntokens)
        # loss_node = loss_node / accum_iter
        if mode == "train" or mode == "train+log":
            loss_node.backward()
            train_state.step += 1
            train_state.samples += batch.src.shape[0]
            train_state.tokens += batch.ntokens
            if i % accum_iter == 0:
                optimizer.step()
                optimizer.zero_grad(set_to_none=True)
                n_accum += 1
                train_state.accum_step += 1
            scheduler.step()

        total_loss += loss
        total_tokens += batch.ntokens
        tokens += batch.ntokens
        if i % 40 == 1 and (mode == "train" or mode == "train+log"):
            lr = optimizer.param_groups[0]["lr"]
            elapsed = time.time() - start
            print(
                (
                    "Epoch Step: %6d | Accumulation Step: %3d | Loss: %6.2f "
                    + "| Tokens / Sec: %7.1f | Learning Rate: %6.1e"
                )
                % (i, n_accum, loss / batch.ntokens, tokens / elapsed, lr)
            )
            start = time.time()
            tokens = 0
        del loss
        del loss_node
    return total_loss / total_tokens, train_state


# %% [markdown] id="aB1IF0foTsqJ"
# ## Training Data and Batching
#
# We trained on the standard WMT 2014 English-German dataset
# consisting of about 4.5 million sentence pairs.  Sentences were
# encoded using byte-pair encoding, which has a shared source-target
# vocabulary of about 37000 tokens. For English-French, we used the
# significantly larger WMT 2014 English-French dataset consisting of
# 36M sentences and split tokens into a 32000 word-piece vocabulary.
#
#
# Sentence pairs were batched together by approximate sequence length.
# Each training batch contained a set of sentence pairs containing
# approximately 25000 source tokens and 25000 target tokens.

# %% [markdown] id="F1mTQatiTsqJ" jp-MarkdownHeadingCollapsed=true tags=[]
# ## Hardware and Schedule
#
# We trained our models on one machine with 8 NVIDIA P100 GPUs.  For
# our base models using the hyperparameters described throughout the
# paper, each training step took about 0.4 seconds.  We trained the
# base models for a total of 100,000 steps or 12 hours. For our big
# models, step time was 1.0 seconds.  The big models were trained for
# 300,000 steps (3.5 days).

# %% [markdown] id="-utZeuGcTsqJ"
# ## Optimizer
#
# We used the Adam optimizer [(cite)](https://arxiv.org/abs/1412.6980)
# with $\beta_1=0.9$, $\beta_2=0.98$ and $\epsilon=10^{-9}$.  We
# varied the learning rate over the course of training, according to
# the formula:
#
# $$
# lrate = d_{\text{model}}^{-0.5} \cdot
#   \min({step\_num}^{-0.5},
#     {step\_num} \cdot {warmup\_steps}^{-1.5})
# $$
#
# This corresponds to increasing the learning rate linearly for the
# first $warmup\_steps$ training steps, and decreasing it thereafter
# proportionally to the inverse square root of the step number.  We
# used $warmup\_steps=4000$.

# %% [markdown] id="39FbYnt-TsqJ"
#
# > Note: This part is very important. Need to train with this setup
# > of the model.

# %% [markdown] id="hlbojFkjTsqJ"
#
# > Example of the curves of this model for different model sizes and
# > for optimization hyperparameters.

# %% id="zUz3PdAnVg4o"
def rate(step, model_size, factor, warmup):
    """
    we have to default the step to 1 for LambdaLR function
    to avoid zero raising to negative power.
    """
    if step == 0:
        step = 1
    return factor * (
        model_size ** (-0.5) * min(step ** (-0.5), step * warmup ** (-1.5))
    )


# %% id="l1bnrlnSV8J5" tags=[]
def example_learning_schedule():
    opts = [
        [512, 1, 4000],  # example 1
        [512, 1, 8000],  # example 2
        [256, 1, 4000],  # example 3
    ]

    dummy_model = torch.nn.Linear(1, 1)
    learning_rates = []

    # we have 3 examples in opts list.
    for idx, example in enumerate(opts):
        # run 20000 epoch for each example
        optimizer = torch.optim.Adam(
            dummy_model.parameters(), lr=1, betas=(0.9, 0.98), eps=1e-9
        )
        lr_scheduler = LambdaLR(
            optimizer=optimizer, lr_lambda=lambda step: rate(step, *example)
        )
        tmp = []
        # take 20K dummy training steps, save the learning rate at each step
        for step in range(20000):
            tmp.append(optimizer.param_groups[0]["lr"])
            optimizer.step()
            lr_scheduler.step()
        learning_rates.append(tmp)

    learning_rates = torch.tensor(learning_rates)

    # Enable altair to handle more than 5000 rows
    alt.data_transformers.disable_max_rows()

    opts_data = pd.concat(
        [
            pd.DataFrame(
                {
                    "Learning Rate": learning_rates[warmup_idx, :],
                    "model_size:warmup": ["512:4000", "512:8000", "256:4000"][
                        warmup_idx
                    ],
                    "step": range(20000),
                }
            )
            for warmup_idx in [0, 1, 2]
        ]
    )

    return (
        alt.Chart(opts_data)
        .mark_line()
        .properties(width=600)
        .encode(x="step", y="Learning Rate", color="model_size:warmup:N")
        .interactive()
    )


example_learning_schedule()


# %% [markdown] id="7T1uD15VTsqK"
# ## Regularization
#
# ### Label Smoothing
#
# During training, we employed label smoothing of value
# $\epsilon_{ls}=0.1$ [(cite)](https://arxiv.org/abs/1512.00567).
# This hurts perplexity, as the model learns to be more unsure, but
# improves accuracy and BLEU score.

# %% [markdown] id="kNoAVD8bTsqK"
#
# > We implement label smoothing using the KL div loss. Instead of
# > using a one-hot target distribution, we create a distribution that
# > has `confidence` of the correct word and the rest of the
# > `smoothing` mass distributed throughout the vocabulary.

# %% id="shU2GyiETsqK"
class LabelSmoothing(nn.Module):
    "Implement label smoothing."

    def __init__(self, size, padding_idx, smoothing=0.0):
        super(LabelSmoothing, self).__init__()
        self.criterion = nn.KLDivLoss(reduction="sum")
        self.padding_idx = padding_idx
        self.confidence = 1.0 - smoothing
        self.smoothing = smoothing
        self.size = size
        self.true_dist = None

    def forward(self, x, target):
        assert x.size(1) == self.size
        true_dist = x.data.clone()
        true_dist.fill_(self.smoothing / (self.size - 2))
        true_dist.scatter_(1, target.data.unsqueeze(1), self.confidence)
        true_dist[:, self.padding_idx] = 0
        mask = torch.nonzero(target.data == self.padding_idx)
        if mask.dim() > 0:
            true_dist.index_fill_(0, mask.squeeze(), 0.0)
        self.true_dist = true_dist
        return self.criterion(x, true_dist.clone().detach())


# %% [markdown] id="jCxUrlUyTsqK"
#
# > Here we can see an example of how the mass is distributed to the
# > words based on confidence.

# %% id="EZtKaaQNTsqK"
# Example of label smoothing.


def example_label_smoothing():
    crit = LabelSmoothing(5, 0, 0.4)
    predict = torch.FloatTensor(
        [
            [0, 0.2, 0.7, 0.1, 0],
            [0, 0.2, 0.7, 0.1, 0],
            [0, 0.2, 0.7, 0.1, 0],
            [0, 0.2, 0.7, 0.1, 0],
            [0, 0.2, 0.7, 0.1, 0],
        ]
    )
    crit(x=predict.log(), target=torch.LongTensor([2, 1, 0, 3, 3]))
    LS_data = pd.concat(
        [
            pd.DataFrame(
                {
                    "target distribution": crit.true_dist[x, y].flatten(),
                    "columns": y,
                    "rows": x,
                }
            )
            for y in range(5)
            for x in range(5)
        ]
    )

    return (
        alt.Chart(LS_data)
        .mark_rect(color="Blue", opacity=1)
        .properties(height=200, width=200)
        .encode(
            alt.X("columns:O", title=None),
            alt.Y("rows:O", title=None),
            alt.Color(
                "target distribution:Q", scale=alt.Scale(scheme="viridis")
            ),
        )
        .interactive()
    )


show_example(example_label_smoothing)


# %% [markdown] id="CGM8J1veTsqK"
#
# > Label smoothing actually starts to penalize the model if it gets
# > very confident about a given choice.

# %% id="78EHzLP7TsqK"


def loss(x, crit):
    d = x + 3 * 1
    predict = torch.FloatTensor([[0, x / d, 1 / d, 1 / d, 1 / d]])
    return crit(predict.log(), torch.LongTensor([1])).data


def penalization_visualization():
    crit = LabelSmoothing(5, 0, 0.1)
    loss_data = pd.DataFrame(
        {
            "Loss": [loss(x, crit) for x in range(1, 100)],
            "Steps": list(range(99)),
        }
    ).astype("float")

    return (
        alt.Chart(loss_data)
        .mark_line()
        .properties(width=350)
        .encode(
            x="Steps",
            y="Loss",
        )
        .interactive()
    )


show_example(penalization_visualization)


# %% [markdown] id="67lUqeLXTsqK"
# # A First  Example
#
# > We can begin by trying out a simple copy-task. Given a random set
# > of input symbols from a small vocabulary, the goal is to generate
# > back those same symbols.

# %% [markdown] id="jJa-89_pTsqK"
# ## Synthetic Data

# %% id="g1aTxeqqTsqK"
def data_gen(V, batch_size, nbatches):
    "Generate random data for a src-tgt copy task."
    for i in range(nbatches):
        data = torch.randint(1, V, size=(batch_size, 10))
        data[:, 0] = 1
        src = data.requires_grad_(False).clone().detach()
        tgt = data.requires_grad_(False).clone().detach()
        yield Batch(src, tgt, 0)


# %% [markdown] id="XTXwD9hUTsqK"
# ## Loss Computation

# %% id="3J8EJm87TsqK"
class SimpleLossCompute:
    "A simple loss compute and train function."

    def __init__(self, generator, criterion):
        self.generator = generator
        self.criterion = criterion

    def __call__(self, x, y, norm):
        x = self.generator(x)
        sloss = (
            self.criterion(
                x.contiguous().view(-1, x.size(-1)), y.contiguous().view(-1)
            )
            / norm
        )
        return sloss.data * norm, sloss


# %% [markdown] id="eDAI7ELUTsqL"
# ## Greedy Decoding

# %% [markdown] id="LFkWakplTsqL" tags=[]
# > This code predicts a translation using greedy decoding for simplicity.
# %% id="N2UOpnT3bIyU"
def greedy_decode(model, src, src_mask, max_len, start_symbol):
    memory = model.encode(src, src_mask)
    ys = torch.zeros(1, 1).fill_(start_symbol).type_as(src.data)
    for i in range(max_len - 1):
        out = model.decode(
            memory, src_mask, ys, subsequent_mask(ys.size(1)).type_as(src.data)
        )
        prob = model.generator(out[:, -1])
        _, next_word = torch.max(prob, dim=1)
        next_word = next_word.data[0]
        ys = torch.cat(
            [ys, torch.zeros(1, 1).type_as(src.data).fill_(next_word)], dim=1
        )
    return ys


# %% id="qgIZ2yEtdYwe" tags=[]
# Train the simple copy task.


def example_simple_model():
    V = 11
    criterion = LabelSmoothing(size=V, padding_idx=0, smoothing=0.0)
    model = make_model(V, V, N=2)

    optimizer = torch.optim.Adam(
        model.parameters(), lr=0.5, betas=(0.9, 0.98), eps=1e-9
    )
    lr_scheduler = LambdaLR(
        optimizer=optimizer,
        lr_lambda=lambda step: rate(
            step, model_size=model.src_embed[0].d_model, factor=1.0, warmup=400
        ),
    )

    batch_size = 80
    for epoch in range(20):
        model.train()
        run_epoch(
            data_gen(V, batch_size, 20),
            model,
            SimpleLossCompute(model.generator, criterion),
            optimizer,
            lr_scheduler,
            mode="train",
        )
        model.eval()
        run_epoch(
            data_gen(V, batch_size, 5),
            model,
            SimpleLossCompute(model.generator, criterion),
            DummyOptimizer(),
            DummyScheduler(),
            mode="eval",
        )[0]

    model.eval()
    src = torch.LongTensor([[0, 1, 2, 3, 4, 5, 6, 7, 8, 9]])
    max_len = src.shape[1]
    src_mask = torch.ones(1, 1, max_len)
    print(greedy_decode(model, src, src_mask, max_len=max_len, start_symbol=0))


execute_example(example_simple_model)


# %% [markdown] id="OpuQv2GsTsqL"
# # Part 3: A Real World Example
#
# > Now we consider a real-world example using the Multi30k
# > German-English Translation task. This task is much smaller than
# > the WMT task considered in the paper, but it illustrates the whole
# > system. We also show how to use multi-gpu processing to make it
# > really fast.

# %% [markdown] id="8y9dpfolTsqL" tags=[]
# ## Data Loading
#
# > We will load the dataset using torchtext and spacy for
# > tokenization.

# %%
# Load spacy tokenizer models, download them if they haven't been
# downloaded already


# def load_tokenizers():

#     try:
#         spacy_de = spacy.load("de_core_news_sm")
#     except IOError:
#         os.system("python -m spacy download de_core_news_sm")
#         spacy_de = spacy.load("de_core_news_sm")

#     try:
#         spacy_en = spacy.load("en_core_web_sm")
#     except IOError:
#         os.system("python -m spacy download en_core_web_sm")
#         spacy_en = spacy.load("en_core_web_sm")

#     return spacy_de, spacy_en


# # %% id="t4BszXXJTsqL" tags=[]
# def tokenize(text, tokenizer):
#     return [tok.text for tok in tokenizer.tokenizer(text)]


# def yield_tokens(data_iter, tokenizer, index):
#     for from_to_tuple in data_iter:
#         yield tokenizer(from_to_tuple[index])


# # %% id="jU3kVlV5okC-" tags=[]


# def build_vocabulary(spacy_de, spacy_en):
#     def tokenize_de(text):
#         return tokenize(text, spacy_de)

#     def tokenize_en(text):
#         return tokenize(text, spacy_en)

#     print("Building German Vocabulary ...")
#     train, val, test = datasets.Multi30k(language_pair=("de", "en"))
#     vocab_src = build_vocab_from_iterator(
#         yield_tokens(train + val + test, tokenize_de, index=0),
#         min_freq=2,
#         specials=["<s>", "</s>", "<blank>", "<unk>"],
#     )

#     print("Building English Vocabulary ...")
#     train, val, test = datasets.Multi30k(language_pair=("de", "en"))
#     vocab_tgt = build_vocab_from_iterator(
#         yield_tokens(train + val + test, tokenize_en, index=1),
#         min_freq=2,
#         specials=["<s>", "</s>", "<blank>", "<unk>"],
#     )

#     vocab_src.set_default_index(vocab_src["<unk>"])
#     vocab_tgt.set_default_index(vocab_tgt["<unk>"])

#     return vocab_src, vocab_tgt


# def load_vocab(spacy_de, spacy_en):
#     if not exists("vocab.pt"):
#         vocab_src, vocab_tgt = build_vocabulary(spacy_de, spacy_en)
#         torch.save((vocab_src, vocab_tgt), "vocab.pt")
#     else:
#         vocab_src, vocab_tgt = torch.load("vocab.pt")
#     print("Finished.\nVocabulary sizes:")
#     print(len(vocab_src))
#     print(len(vocab_tgt))
#     return vocab_src, vocab_tgt


# if is_interactive_notebook():
#     # global variables used later in the script
#     spacy_de, spacy_en = show_example(load_tokenizers)
#     vocab_src, vocab_tgt = show_example(load_vocab, args=[spacy_de, spacy_en])


# # %% [markdown] id="-l-TFwzfTsqL"
# #
# # > Batching matters a ton for speed. We want to have very evenly
# # > divided batches, with absolutely minimal padding. To do this we
# # > have to hack a bit around the default torchtext batching. This
# # > code patches their default batching to make sure we search over
# # > enough sentences to find tight batches.

# # %% [markdown] id="kDEj-hCgokC-" tags=[] jp-MarkdownHeadingCollapsed=true
# # ## Iterators

# # %% id="wGsIHFgOokC_" tags=[]
# def collate_batch(
#     batch,
#     src_pipeline,
#     tgt_pipeline,
#     src_vocab,
#     tgt_vocab,
#     device,
#     max_padding=128,
#     pad_id=2,
# ):
#     bs_id = torch.tensor([0], device=device)  # <s> token id
#     eos_id = torch.tensor([1], device=device)  # </s> token id
#     src_list, tgt_list = [], []
#     for (_src, _tgt) in batch:
#         processed_src = torch.cat(
#             [
#                 bs_id,
#                 torch.tensor(
#                     src_vocab(src_pipeline(_src)),
#                     dtype=torch.int64,
#                     device=device,
#                 ),
#                 eos_id,
#             ],
#             0,
#         )
#         processed_tgt = torch.cat(
#             [
#                 bs_id,
#                 torch.tensor(
#                     tgt_vocab(tgt_pipeline(_tgt)),
#                     dtype=torch.int64,
#                     device=device,
#                 ),
#                 eos_id,
#             ],
#             0,
#         )
#         src_list.append(
#             # warning - overwrites values for negative values of padding - len
#             pad(
#                 processed_src,
#                 (
#                     0,
#                     max_padding - len(processed_src),
#                 ),
#                 value=pad_id,
#             )
#         )
#         tgt_list.append(
#             pad(
#                 processed_tgt,
#                 (0, max_padding - len(processed_tgt)),
#                 value=pad_id,
#             )
#         )

#     src = torch.stack(src_list)
#     tgt = torch.stack(tgt_list)
#     return (src, tgt)


# # %% id="ka2Ce_WIokC_" tags=[]
# def create_dataloaders(
#     device,
#     vocab_src,
#     vocab_tgt,
#     spacy_de,
#     spacy_en,
#     batch_size=12000,
#     max_padding=128,
#     is_distributed=True,
# ):
#     # def create_dataloaders(batch_size=12000):
#     def tokenize_de(text):
#         return tokenize(text, spacy_de)

#     def tokenize_en(text):
#         return tokenize(text, spacy_en)

#     def collate_fn(batch):
#         return collate_batch(
#             batch,
#             tokenize_de,
#             tokenize_en,
#             vocab_src,
#             vocab_tgt,
#             device,
#             max_padding=max_padding,
#             pad_id=vocab_src.get_stoi()["<blank>"],
#         )

#     train_iter, valid_iter, test_iter = datasets.Multi30k(
#         language_pair=("de", "en")
#     )

#     train_iter_map = to_map_style_dataset(
#         train_iter
#     )  # DistributedSampler needs a dataset len()
#     train_sampler = (
#         DistributedSampler(train_iter_map) if is_distributed else None
#     )
#     valid_iter_map = to_map_style_dataset(valid_iter)
#     valid_sampler = (
#         DistributedSampler(valid_iter_map) if is_distributed else None
#     )

#     train_dataloader = DataLoader(
#         train_iter_map,
#         batch_size=batch_size,
#         shuffle=(train_sampler is None),
#         sampler=train_sampler,
#         collate_fn=collate_fn,
#     )
#     valid_dataloader = DataLoader(
#         valid_iter_map,
#         batch_size=batch_size,
#         shuffle=(valid_sampler is None),
#         sampler=valid_sampler,
#         collate_fn=collate_fn,
#     )
#     return train_dataloader, valid_dataloader


# # %% [markdown] id="90qM8RzCTsqM"
# # ## Training the System

# # %%
# def train_worker(
#     gpu,
#     ngpus_per_node,
#     vocab_src,
#     vocab_tgt,
#     spacy_de,
#     spacy_en,
#     config,
#     is_distributed=False,
# ):
#     print(f"Train worker process using GPU: {gpu} for training", flush=True)
#     torch.cuda.set_device(gpu)

#     pad_idx = vocab_tgt["<blank>"]
#     d_model = 512
#     model = make_model(len(vocab_src), len(vocab_tgt), N=6)
#     model.cuda(gpu)
#     module = model
#     is_main_process = True
#     if is_distributed:
#         dist.init_process_group(
#             "nccl", init_method="env://", rank=gpu, world_size=ngpus_per_node
#         )
#         model = DDP(model, device_ids=[gpu])
#         module = model.module
#         is_main_process = gpu == 0

#     criterion = LabelSmoothing(
#         size=len(vocab_tgt), padding_idx=pad_idx, smoothing=0.1
#     )
#     criterion.cuda(gpu)

#     train_dataloader, valid_dataloader = create_dataloaders(
#         gpu,
#         vocab_src,
#         vocab_tgt,
#         spacy_de,
#         spacy_en,
#         batch_size=config["batch_size"] // ngpus_per_node,
#         max_padding=config["max_padding"],
#         is_distributed=is_distributed,
#     )

#     optimizer = torch.optim.Adam(
#         model.parameters(), lr=config["base_lr"], betas=(0.9, 0.98), eps=1e-9
#     )
#     lr_scheduler = LambdaLR(
#         optimizer=optimizer,
#         lr_lambda=lambda step: rate(
#             step, d_model, factor=1, warmup=config["warmup"]
#         ),
#     )
#     train_state = TrainState()

#     for epoch in range(config["num_epochs"]):
#         if is_distributed:
#             train_dataloader.sampler.set_epoch(epoch)
#             valid_dataloader.sampler.set_epoch(epoch)

#         model.train()
#         print(f"[GPU{gpu}] Epoch {epoch} Training ====", flush=True)
#         _, train_state = run_epoch(
#             (Batch(b[0], b[1], pad_idx) for b in train_dataloader),
#             model,
#             SimpleLossCompute(module.generator, criterion),
#             optimizer,
#             lr_scheduler,
#             mode="train+log",
#             accum_iter=config["accum_iter"],
#             train_state=train_state,
#         )

#         GPUtil.showUtilization()
#         if is_main_process:
#             file_path = "%s%.2d.pt" % (config["file_prefix"], epoch)
#             torch.save(module.state_dict(), file_path)
#         torch.cuda.empty_cache()

#         print(f"[GPU{gpu}] Epoch {epoch} Validation ====", flush=True)
#         model.eval()
#         sloss = run_epoch(
#             (Batch(b[0], b[1], pad_idx) for b in valid_dataloader),
#             model,
#             SimpleLossCompute(module.generator, criterion),
#             DummyOptimizer(),
#             DummyScheduler(),
#             mode="eval",
#         )
#         print(sloss)
#         torch.cuda.empty_cache()

#     if is_main_process:
#         file_path = "%sfinal.pt" % config["file_prefix"]
#         torch.save(module.state_dict(), file_path)


# # %% tags=[]
# def train_distributed_model(vocab_src, vocab_tgt, spacy_de, spacy_en, config):
#     from the_annotated_transformer import train_worker

#     ngpus = torch.cuda.device_count()
#     os.environ["MASTER_ADDR"] = "localhost"
#     os.environ["MASTER_PORT"] = "12356"
#     print(f"Number of GPUs detected: {ngpus}")
#     print("Spawning training processes ...")
#     mp.spawn(
#         train_worker,
#         nprocs=ngpus,
#         args=(ngpus, vocab_src, vocab_tgt, spacy_de, spacy_en, config, True),
#     )


# def train_model(vocab_src, vocab_tgt, spacy_de, spacy_en, config):
#     if config["distributed"]:
#         train_distributed_model(
#             vocab_src, vocab_tgt, spacy_de, spacy_en, config
#         )
#     else:
#         train_worker(
#             0, 1, vocab_src, vocab_tgt, spacy_de, spacy_en, config, False
#         )


# def load_trained_model():
#     config = {
#         "batch_size": 32,
#         "distributed": False,
#         "num_epochs": 8,
#         "accum_iter": 10,
#         "base_lr": 1.0,
#         "max_padding": 72,
#         "warmup": 3000,
#         "file_prefix": "multi30k_model_",
#     }
#     model_path = "multi30k_model_final.pt"
#     if not exists(model_path):
#         train_model(vocab_src, vocab_tgt, spacy_de, spacy_en, config)

#     model = make_model(len(vocab_src), len(vocab_tgt), N=6)
#     model.load_state_dict(torch.load("multi30k_model_final.pt"))
#     return model


# if is_interactive_notebook():
#     model = load_trained_model()


# # %% [markdown] id="RZK_VjDPTsqN"
# #
# # > Once trained we can decode the model to produce a set of
# # > translations. Here we simply translate the first sentence in the
# # > validation set. This dataset is pretty small so the translations
# # > with greedy search are reasonably accurate.

# # %% [markdown] id="L50i0iEXTsqN"
# # # Additional Components: BPE, Search, Averaging

# # %% [markdown] id="NBx1C2_NTsqN"
# #
# # > So this mostly covers the transformer model itself. There are four
# # > aspects that we didn't cover explicitly. We also have all these
# # > additional features implemented in
# # > [OpenNMT-py](https://github.com/opennmt/opennmt-py).
# #
# #

# # %% [markdown] id="UpqV1mWnTsqN"
# #
# # > 1) BPE/ Word-piece: We can use a library to first preprocess the
# # > data into subword units. See Rico Sennrich's
# # > [subword-nmt](https://github.com/rsennrich/subword-nmt)
# # > implementation. These models will transform the training data to
# # > look like this:

# # %% [markdown] id="hwJ_9J0BTsqN"
# # ▁Die ▁Protokoll datei ▁kann ▁ heimlich ▁per ▁E - Mail ▁oder ▁FTP
# # ▁an ▁einen ▁bestimmte n ▁Empfänger ▁gesendet ▁werden .

# # %% [markdown] id="9HwejYkpTsqN"
# #
# # > 2) Shared Embeddings: When using BPE with shared vocabulary we can
# # > share the same weight vectors between the source / target /
# # > generator. See the [(cite)](https://arxiv.org/abs/1608.05859) for
# # > details. To add this to the model simply do this:

# # %% id="tb3j3CYLTsqN" tags=[]
# if False:
#     model.src_embed[0].lut.weight = model.tgt_embeddings[0].lut.weight
#     model.generator.lut.weight = model.tgt_embed[0].lut.weight


# # %% [markdown] id="xDKJsSwRTsqN"
# #
# # > 3) Beam Search: This is a bit too complicated to cover here. See the
# # > [OpenNMT-py](https://github.com/OpenNMT/OpenNMT-py/)
# # > for a pytorch implementation.
# # >
# #

# # %% [markdown] id="wf3vVYGZTsqN"
# #
# # > 4) Model Averaging: The paper averages the last k checkpoints to
# # > create an ensembling effect. We can do this after the fact if we
# # > have a bunch of models:

# # %% id="hAFEa78JokDB"
# def average(model, models):
#     "Average models into model"
#     for ps in zip(*[m.params() for m in [model] + models]):
#         ps[0].copy_(torch.sum(*ps[1:]) / len(ps[1:]))


# # %% [markdown] id="Kz5BYJ9sTsqO"
# # # Results
# #
# # On the WMT 2014 English-to-German translation task, the big
# # transformer model (Transformer (big) in Table 2) outperforms the
# # best previously reported models (including ensembles) by more than
# # 2.0 BLEU, establishing a new state-of-the-art BLEU score of
# # 28.4. The configuration of this model is listed in the bottom line
# # of Table 3. Training took 3.5 days on 8 P100 GPUs. Even our base
# # model surpasses all previously published models and ensembles, at a
# # fraction of the training cost of any of the competitive models.
# #
# # On the WMT 2014 English-to-French translation task, our big model
# # achieves a BLEU score of 41.0, outperforming all of the previously
# # published single models, at less than 1/4 the training cost of the
# # previous state-of-the-art model. The Transformer (big) model trained
# # for English-to-French used dropout rate Pdrop = 0.1, instead of 0.3.
# #

# # %% [markdown]
# # ![](images/results.png)

# # %% [markdown] id="cPcnsHvQTsqO"
# #
# #
# # > With the addtional extensions in the last section, the OpenNMT-py
# # > replication gets to 26.9 on EN-DE WMT. Here I have loaded in those
# # > parameters to our reimplemenation.

# # %%
# # Load data and model for output checks


# # %%
# def check_outputs(
#     valid_dataloader,
#     model,
#     vocab_src,
#     vocab_tgt,
#     n_examples=15,
#     pad_idx=2,
#     eos_string="</s>",
# ):
#     results = [()] * n_examples
#     for idx in range(n_examples):
#         print("\nExample %d ========\n" % idx)
#         b = next(iter(valid_dataloader))
#         rb = Batch(b[0], b[1], pad_idx)
#         greedy_decode(model, rb.src, rb.src_mask, 64, 0)[0]

#         src_tokens = [
#             vocab_src.get_itos()[x] for x in rb.src[0] if x != pad_idx
#         ]
#         tgt_tokens = [
#             vocab_tgt.get_itos()[x] for x in rb.tgt[0] if x != pad_idx
#         ]

#         print(
#             "Source Text (Input)        : "
#             + " ".join(src_tokens).replace("\n", "")
#         )
#         print(
#             "Target Text (Ground Truth) : "
#             + " ".join(tgt_tokens).replace("\n", "")
#         )
#         model_out = greedy_decode(model, rb.src, rb.src_mask, 72, 0)[0]
#         model_txt = (
#             " ".join(
#                 [vocab_tgt.get_itos()[x] for x in model_out if x != pad_idx]
#             ).split(eos_string, 1)[0]
#             + eos_string
#         )
#         print("Model Output               : " + model_txt.replace("\n", ""))
#         results[idx] = (rb, src_tokens, tgt_tokens, model_out, model_txt)
#     return results


# def run_model_example(n_examples=5):
#     global vocab_src, vocab_tgt, spacy_de, spacy_en

#     print("Preparing Data ...")
#     _, valid_dataloader = create_dataloaders(
#         torch.device("cpu"),
#         vocab_src,
#         vocab_tgt,
#         spacy_de,
#         spacy_en,
#         batch_size=1,
#         is_distributed=False,
#     )

#     print("Loading Trained Model ...")

#     model = make_model(len(vocab_src), len(vocab_tgt), N=6)
#     model.load_state_dict(
#         torch.load("multi30k_model_final.pt", map_location=torch.device("cpu"))
#     )

#     print("Checking Model Outputs:")
#     example_data = check_outputs(
#         valid_dataloader, model, vocab_src, vocab_tgt, n_examples=n_examples
#     )
#     return model, example_data


# # execute_example(run_model_example)


# # %% [markdown] id="0ZkkNTKLTsqO"
# # ## Attention Visualization
# #
# # > Even with a greedy decoder the translation looks pretty good. We
# # > can further visualize it to see what is happening at each layer of
# # > the attention

# # %%
# def mtx2df(m, max_row, max_col, row_tokens, col_tokens):
#     "convert a dense matrix to a data frame with row and column indices"
#     return pd.DataFrame(
#         [
#             (
#                 r,
#                 c,
#                 float(m[r, c]),
#                 "%.3d %s"
#                 % (r, row_tokens[r] if len(row_tokens) > r else "<blank>"),
#                 "%.3d %s"
#                 % (c, col_tokens[c] if len(col_tokens) > c else "<blank>"),
#             )
#             for r in range(m.shape[0])
#             for c in range(m.shape[1])
#             if r < max_row and c < max_col
#         ],
#         # if float(m[r,c]) != 0 and r < max_row and c < max_col],
#         columns=["row", "column", "value", "row_token", "col_token"],
#     )


# def attn_map(attn, layer, head, row_tokens, col_tokens, max_dim=30):
#     df = mtx2df(
#         attn[0, head].data,
#         max_dim,
#         max_dim,
#         row_tokens,
#         col_tokens,
#     )
#     return (
#         alt.Chart(data=df)
#         .mark_rect()
#         .encode(
#             x=alt.X("col_token", axis=alt.Axis(title="")),
#             y=alt.Y("row_token", axis=alt.Axis(title="")),
#             color="value",
#             tooltip=["row", "column", "value", "row_token", "col_token"],
#         )
#         .properties(height=400, width=400)
#         .interactive()
#     )


# # %% tags=[]
# def get_encoder(model, layer):
#     return model.encoder.layers[layer].self_attn.attn


# def get_decoder_self(model, layer):
#     return model.decoder.layers[layer].self_attn.attn


# def get_decoder_src(model, layer):
#     return model.decoder.layers[layer].src_attn.attn


# def visualize_layer(model, layer, getter_fn, ntokens, row_tokens, col_tokens):
#     # ntokens = last_example[0].ntokens
#     attn = getter_fn(model, layer)
#     n_heads = attn.shape[1]
#     charts = [
#         attn_map(
#             attn,
#             0,
#             h,
#             row_tokens=row_tokens,
#             col_tokens=col_tokens,
#             max_dim=ntokens,
#         )
#         for h in range(n_heads)
#     ]
#     assert n_heads == 8
#     return alt.vconcat(
#         charts[0]
#         # | charts[1]
#         | charts[2]
#         # | charts[3]
#         | charts[4]
#         # | charts[5]
#         | charts[6]
#         # | charts[7]
#         # layer + 1 due to 0-indexing
#     ).properties(title="Layer %d" % (layer + 1))


# # %% [markdown]
# # ## Encoder Self Attention

# # %% tags=[]
# def viz_encoder_self():
#     model, example_data = run_model_example(n_examples=1)
#     example = example_data[
#         len(example_data) - 1
#     ]  # batch object for the final example

#     layer_viz = [
#         visualize_layer(
#             model, layer, get_encoder, len(example[1]), example[1], example[1]
#         )
#         for layer in range(6)
#     ]
#     return alt.hconcat(
#         layer_viz[0]
#         # & layer_viz[1]
#         & layer_viz[2]
#         # & layer_viz[3]
#         & layer_viz[4]
#         # & layer_viz[5]
#     )


# show_example(viz_encoder_self)


# # %% [markdown]
# # ## Decoder Self Attention

# # %% tags=[]
# def viz_decoder_self():
#     model, example_data = run_model_example(n_examples=1)
#     example = example_data[len(example_data) - 1]

#     layer_viz = [
#         visualize_layer(
#             model,
#             layer,
#             get_decoder_self,
#             len(example[1]),
#             example[1],
#             example[1],
#         )
#         for layer in range(6)
#     ]
#     return alt.hconcat(
#         layer_viz[0]
#         & layer_viz[1]
#         & layer_viz[2]
#         & layer_viz[3]
#         & layer_viz[4]
#         & layer_viz[5]
#     )


# show_example(viz_decoder_self)


# # %% [markdown]
# # ## Decoder Src Attention

# # %% tags=[]
# def viz_decoder_src():
#     model, example_data = run_model_example(n_examples=1)
#     example = example_data[len(example_data) - 1]

#     layer_viz = [
#         visualize_layer(
#             model,
#             layer,
#             get_decoder_src,
#             max(len(example[1]), len(example[2])),
#             example[1],
#             example[2],
#         )
#         for layer in range(6)
#     ]
#     return alt.hconcat(
#         layer_viz[0]
#         & layer_viz[1]
#         & layer_viz[2]
#         & layer_viz[3]
#         & layer_viz[4]
#         & layer_viz[5]
#     )


# show_example(viz_decoder_src)

# # %% [markdown] id="nSseuCcATsqO"
# # # Conclusion
# #
# #  Hopefully this code is useful for future research. Please reach
# #  out if you have any issues.
# #
# #
# #  Cheers,
# #  Sasha Rush, Austin Huang, Suraj Subramanian, Jonathan Sum, Khalid Almubarak,
# #  Stella Biderman