prompt_front: You are given a scientific article and a question. Answer the question as concisely as you can, using a single phrase or sentence if possible. If the question cannot be answered based on the information in the article, write "unanswerable". If the question is a yes/no question, answer "yes", "no", or "unanswerable". Do not provide any explanation.

Please answer the questions based on the text provided below. How are weights dynamically adjusted?
Context 1: Introduction
Data imbalance is a common issue in a variety of NLP tasks such as tagging and machine reading comprehension  Table TABREF3 gives concrete examples: for the Named Entity Recognition (NER) task BIBREF2, BIBREF3, most tokens are backgrounds with tagging class $O$  Specifically, the number of tokens tagging class $O$ is 5 times as many as those with entity labels for the CoNLL03 dataset and 8 times for the OntoNotes5 0 dataset; Data-imbalanced issue is more severe for MRC tasks BIBREF4, BIBREF5, BIBREF6, BIBREF7, BIBREF8 with the value of negative-positive ratio being 50-200 
Data imbalance results in the following two issues: (1) the training-test discrepancy: Without balancing the labels, the learning process tends to converge to a point that strongly biases towards class with the majority label  This actually creates a discrepancy between training and test: at training time, each training instance contributes equally to the objective function while at test time, F1 score concerns more about positive examples; (2) the overwhelming effect of easy-negative examples  As pointed out by meng2019dsreg, significantly large number of negative examples also means that the number of easy-negative example is large  The huge number of easy examples tends to overwhelm the training, making the model not sufficiently learned to distinguish between positive examples and hard-negative examples  The cross-entropy objective (CE for short) or maximum likelihood (MLE) objective, which is widely adopted as the training objective for data-imbalanced NLP tasks BIBREF9, BIBREF10, BIBREF11, BIBREF12, BIBREF13, BIBREF14, BIBREF15, handles neither of the issues 
To handle the first issue, we propose to replace CE or MLE with losses based on the Sørensen–Dice coefficient BIBREF0 or Tversky index BIBREF1  The Sørensen–Dice coefficient, dice loss for short, is the harmonic mean of precision and recall  It attaches equal importance to false positives (FPs) and false negatives (FNs) and is thus more immune to data-imbalanced datasets  Tversky index extends dice loss by using a weight that trades precision and recall, which can be thought as the approximation of the $F_{\beta }$ score, and thus comes with more flexibility  Therefore, We use dice loss or Tversky index to replace CE loss to address the first issue 
Only using dice loss or Tversky index is not enough since they are unable to address the dominating influence of easy-negative examples  This is intrinsically because dice loss is actually a hard version of the F1 score  Taking the binary classification task as an example, at test time, an example will be classified as negative as long as its probability is smaller than 0 5, but training will push the value to 0 as much as possible  This gap isn't a big issue for balanced datasets, but is extremely detrimental if a big proportion of training examples are easy-negative ones: easy-negative examples can easily dominate training since their probabilities can be pushed to 0 fairly easily  Meanwhile, the model can hardly distinguish between hard-negative examples and positive ones  Inspired by the idea of focal loss BIBREF16 in computer vision, we propose a dynamic weight adjusting strategy, which associates each training example with a weight in proportion to $(1-p)$, and this weight dynamically changes as training proceeds  This strategy helps to deemphasize confident examples during training as their $p$ approaches the value of 1, makes the model attentive to hard-negative examples, and thus alleviates the dominating effect of easy-negative examples 
Combing both strategies, we observe significant performance boosts on a wide range of data imbalanced NLP tasks  Notably, we are able to achieve SOTA results on CTB5 (97 92, +1 86), CTB6 (96 57, +1 80) and UD1 4 (96 98, +2 19) for the POS task; SOTA results on CoNLL03 (93 33, +0 29), OntoNotes5 0 (92 07, +0 96)), MSRA 96 72(+0 97) and OntoNotes4 0 (84 47,+2 36) for the NER task; along with competitive results on the tasks of machine reading comprehension and paraphrase identification 
The rest of this paper is organized as follows: related work is presented in Section 2  We describe different training objectives in Section 3  Experimental results are presented in Section 4  We perform ablation studies in Section 5, followed by a brief conclusion in Section 6 
Related Work ::: Data Resample
The idea of weighting training examples has a long history  Importance sampling BIBREF17 assigns weights to different samples and changes the data distribution  Boosting algorithms such as AdaBoost BIBREF18 select harder examples to train subsequent classifiers  Similarly, hard example mining BIBREF19 downsamples the majority class and exploits the most difficult examples  Oversampling BIBREF20, BIBREF21 is used to balance the data distribution  Another line of data resampling is to dynamically control the weights of examples as training proceeds  For example, focal loss BIBREF16 used a soft weighting scheme that emphasizes harder examples during training  In self-paced learning BIBREF22, example weights are obtained through optimizing the weighted training loss which encourages learning easier examples first  At each training step, self-paced learning algorithm optimizes model parameters and example weights jointly  Other works BIBREF23, BIBREF24 adjusted the weights of different training examples based on training loss  Besides, recent work BIBREF25, BIBREF26 proposed to learn a separate network to predict sample weights 
Related Work ::: Data Imbalance Issue in Object Detection
The background-object label imbalance issue is severe and thus well studied in the field of object detection BIBREF27, BIBREF28, BIBREF29, BIBREF30, BIBREF31  The idea of hard negative mining (HNM) BIBREF30 has gained much attention recently  shrivastava2016ohem proposed the online hard example mining (OHEM) algorithm in an iterative manner that makes training progressively more difficult, and pushes the model to learn better  ssd2016liu sorted all of the negative samples based on the confidence loss and picking the training examples with the negative-positive ratio at 3:1  pang2019rcnn proposed a novel method called IoU-balanced sampling and aploss2019chen designed a ranking model to replace the conventional classification task with a average-precision loss to alleviate the class imbalance issue  The efforts made on object detection have greatly inspired us to solve the data imbalance issue in NLP 
Losses ::: Notation
For illustration purposes, we use the binary classification task to demonstrate how different losses work  The mechanism can be easily extended to multi-class classification 
Let $\lbrace x_i\rbrace $ denote a set of instances  Each $x_i$ is associated with a golden label vector $y_i = [y_{i0},y_{i1} ]$, where $y_{i1}\in \lbrace 0,1\rbrace $ and $y_{i0}\in \lbrace 0,1\rbrace $ respectively denote the positive and negative classes, and thus $y_i$ can be either $[0,1]$ or $[0,1]$  Let $p_i = [p_{i0},p_{i1} ]$ denote the probability vector, and $p_{i1}$ and $p_{i0}$ respectively denote the probability that a model assigns the positive and negative label to $x_i$ 
Losses ::: Cross Entropy Loss
The vanilla cross entropy (CE) loss is given by:
As can be seen from Eq DISPLAY_FORM8, each $x_i$ contributes equally to the final objective  Two strategies are normally used to address the the case where we wish that not all $x_i$ are treated equal: associating different classes with different weighting factor $\alpha $ or resampling the datasets  For the former, Eq DISPLAY_FORM8 is adjusted as follows:
where $\alpha _i\in [0,1]$ may be set by the inverse class frequency or treated as a hyperparameter to set by cross validation  In this work, we use $\lg (\frac{n-n_t}{n_t}+K)$ to calculate the coefficient $\alpha $, where $n_t$ is the number of samples with class $t$ and $n$ is the total number of samples in the training set  $K$ is a hyperparameter to tune  The data resampling strategy constructs a new dataset by sampling training examples from the original dataset based on human-designed criteria, e g , extract equal training samples from each class  Both strategies are equivalent to changing the data distribution and thus are of the same nature  Empirically, these two methods are not widely used due to the trickiness of selecting $\alpha $ especially for multi-class classification tasks and that inappropriate selection can easily bias towards rare classes BIBREF32 
Losses ::: Dice coefficient and Tversky index
Sørensen–Dice coefficient BIBREF0, BIBREF33, dice coefficient (DSC) for short, is a F1-oriented statistic used to gauge the similarity of two sets  Given two sets $A$ and $B$, the dice coefficient between them is given as follows:
In our case, $A$ is the set that contains of all positive examples predicted by a specific model, and $B$ is the set of all golden positive examples in the dataset  When applied to boolean data with the definition of true positive (TP), false positive (FP), and false negative (FN), it can be then written as follows:
For an individual example $x_i$, its corresponding DSC loss is given as follows:
As can be seen, for a negative example with $y_{i1}=0$, it does not contribute to the objective  For smoothing purposes, it is common to add a $\gamma $ factor to both the nominator and the denominator, making the form to be as follows:
As can be seen, negative examples, with $y_{i1}$ being 0 and DSC being $\frac{\gamma }{ p_{i1}+\gamma }$, also contribute to the training  Additionally, milletari2016v proposed to change the denominator to the square form for faster convergence, which leads to the following dice loss (DL):
Another version of DL is to directly compute set-level dice coefficient instead of the sum of individual dice coefficient  We choose the latter due to ease of optimization 
Tversky index (TI), which can be thought as the approximation of the $F_{\beta }$ score, extends dice coefficient to a more general case  Given two sets $A$ and $B$, tversky index is computed as follows:
Tversky index offers the flexibility in controlling the tradeoff between false-negatives and false-positives  It degenerates to DSC if $\alpha =\beta =0 5$  The Tversky loss (TL) for the training set $\lbrace x_i,y_i\rbrace $ is thus as follows:
Losses ::: Self-adusting Dice Loss
Consider a simple case where the dataset consists of only one example $x_i$, which is classified as positive as long as $p_{i1}$ is larger than 0 5  The computation of $F1$ score is actually as follows:
Comparing Eq DISPLAY_FORM14 with Eq DISPLAY_FORM22, we can see that Eq DISPLAY_FORM14 is actually a soft form of $F1$, using a continuous $p$ rather than the binary $\mathbb {I}( p_{i1}>0 5)$  This gap isn't a big issue for balanced datasets, but is extremely detrimental if a big proportion of training examples are easy-negative ones: easy-negative examples can easily dominate training since their probabilities can be pushed to 0 fairly easily  Meanwhile, the model can hardly distinguish between hard-negative examples and positive ones, which has a huge negative effect on the final F1 performance 
To address this issue, we propose to multiply the soft probability $p$ with a decaying factor $(1-p)$, changing Eq DISPLAY_FORM22 to the following form:
One can think $(1-p_{i1})$ as a weight associated with each example, which changes as training proceeds  The intuition of changing $p_{i1}$ to $(1-p_{i1}) p_{i1}$ is to push down the weight of easy examples  For easy examples whose probability are approaching 0 or 1, $(1-p_{i1}) p_{i1}$ makes the model attach significantly less focus to them  Figure FIGREF23 gives gives an explanation from the perspective in derivative: the derivative of $\frac{(1-p)p}{1+(1-p)p}$ with respect to $p$ approaches 0 immediately after $p$ approaches 0, which means the model attends less to examples once they are correctly classified 
A close look at Eq DISPLAY_FORM14 reveals that it actually mimics the idea of focal loss (FL for short) BIBREF16 for object detection in vision  Focal loss was proposed for one-stage object detector to handle foreground-background tradeoff encountered during training  It down-weights the loss assigned to well-classified examples by adding a $(1-p)^{\beta }$ factor, leading the final loss to be $(1-p)^{\beta }\log p$ 
In Table TABREF18, we show the losses used in our experiments, which is described in the next section 
Experiments
We evaluate the proposed method on four NLP tasks: part-of-speech tagging, named entity recognition, machine reading comprehension and paraphrase identification  Baselines in our experiments are optimized by using the standard cross-entropy training objective 
Experiments ::: Part-of-Speech Tagging
Part-of-speech tagging (POS) is the task of assigning a label (e g , noun, verb, adjective) to each word in a given text  In this paper, we choose BERT as the backbone and conduct experiments on three Chinese POS datasets  We report the span-level micro-averaged precision, recall and F1 for evaluation  Hyperparameters are tuned on the corresponding development set of each dataset 
Experiments ::: Part-of-Speech Tagging ::: Datasets
We conduct experiments on the widely used Chinese Treebank 5 0, 6 0 as well as UD1 4 
CTB5 is a Chinese dataset for tagging and parsing, which contains 507,222 words, 824,983 characters and 18,782 sentences extracted from newswire sources 
CTB6 is an extension of CTB5, containing 781,351 words, 1,285,149 characters and 28,295 sentences 
UD is the abbreviation of Universal Dependencies, which is a framework for consistent annotation of grammar (parts of speech, morphological features, and syntactic dependencies) across different human languages  In this work, we use UD1 4 for Chinese POS tagging 
Experiments ::: Part-of-Speech Tagging ::: Baselines
We use the following baselines:
Joint-POS: shao2017character jointly learns Chinese word segmentation and POS 
Lattice-LSTM: lattice2018zhang constructs a word-character lattice 
Bert-Tagger: devlin2018bert treats part-of-speech as a tagging task 
Experiments ::: Part-of-Speech Tagging ::: Results
Table presents the experimental results on the POS task  As can be seen, the proposed DSC loss outperforms the best baseline results by a large margin, i e , outperforming BERT-tagger by +1 86 in terms of F1 score on CTB5, +1 80 on CTB6 and +2 19 on UD1 4  As far as we are concerned, we are achieving SOTA performances on the three datasets  Weighted cross entropy and focal loss only gain a little performance improvement on CTB5 and CTB6, and the dice loss obtains huge gain on CTB5 but not on CTB6, which indicates the three losses are not consistently robust in resolving the data imbalance issue  The proposed DSC loss performs robustly on all the three datasets 
Experiments ::: Named Entity Recognition
Named entity recognition (NER) refers to the task of detecting the span and semantic category of entities from a chunk of text  Our implementation uses the current state-of-the-art BERT-MRC model proposed by xiaoya2019ner as a backbone  For English datasets, we use BERT$_\text{Large}$ English checkpoints, while for Chinese we use the official Chinese checkpoints  We report span-level micro-averaged precision, recall and F1-score  Hyperparameters are tuned on the development set of each dataset 
Experiments ::: Named Entity Recognition ::: Datasets
For the NER task, we consider both Chinese datasets, i e , OntoNotes4 0 BIBREF34 and MSRA BIBREF35, and English datasets, i e , CoNLL2003 BIBREF36 and OntoNotes5 0 BIBREF37 
CoNLL2003 is an English dataset with 4 entity types: Location, Organization, Person and Miscellaneous  We followed data processing protocols in BIBREF14 
English OntoNotes5 0 consists of texts from a wide variety of sources and contains 18 entity types  We use the standard train/dev/test split of CoNLL2012 shared task 
Chinese MSRA performs as a Chinese benchmark dataset containing 3 entity types  Data in MSRA is collected from news domain  Since the development set is not provided in the original MSRA dataset, we randomly split the training set into training and development splits by 9:1  We use the official test set for evaluation 
Chinese OntoNotes4 0 is a Chinese dataset and consists of texts from news domain, which has 18 entity types  In this paper, we take the same data split as wu2019glyce did 
Experiments ::: Named Entity Recognition ::: Baselines
We use the following baselines:
ELMo: a tagging model from peters2018deep 
Lattice-LSTM: lattice2018zhang constructs a word-character lattice, only used in Chinese datasets 
CVT: from kevin2018cross, which uses Cross-View Training(CVT) to improve the representations of a Bi-LSTM encoder 
Bert-Tagger: devlin2018bert treats NER as a tagging task 
Glyce-BERT: wu2019glyce combines glyph information with BERT pretraining 
BERT-MRC: The current SOTA model for both Chinese and English NER datasets proposed by xiaoya2019ner, which formulate NER as machine reading comprehension task 
Experiments ::: Named Entity Recognition ::: Results
Table shows experimental results on NER datasets  For English datasets including CoNLL2003 and OntoNotes5 0, our proposed method outperforms BERT-MRCBIBREF38 by +0 29 and +0 96 respectively  We observe huge performance boosts on Chinese datasets, achieving F1 improvements by +0 97 and +2 36 on MSRA and OntoNotes4 0, respectively  As far as we are concerned, we are setting new SOTA performances on all of the four NER datasets 
Experiments ::: Machine Reading Comprehension
Machine reading comprehension (MRC) BIBREF39, BIBREF40, BIBREF41, BIBREF40, BIBREF42, BIBREF15 has become a central task in natural language understanding  MRC in the SQuAD-style is to predict the answer span in the passage given a question and the passage  In this paper, we choose the SQuAD-style MRC task and report Extract Match (EM) in addition to F1 score on validation set  All hyperparameters are tuned on the development set of each dataset 
Experiments ::: Machine Reading Comprehension ::: Datasets
The following five datasets are used for MRC task: SQuAD v1 1, SQuAD v2 0 BIBREF4, BIBREF6 and Quoref BIBREF8 
SQuAD v1 1 and SQuAD v2 0 are the most widely used QA benchmarks  SQuAD1 1 is a collection of 100K crowdsourced question-answer pairs, and SQuAD2 0 extends SQuAD1 1 allowing no short answer exists in the provided passage 
Quoref is a QA dataset which tests the coreferential reasoning capability of reading comprehension systems, containing 24K questions over 4 7K paragraphs from Wikipedia 
Experiments ::: Machine Reading Comprehension ::: Baselines
We use the following baselines:
QANet: qanet2018 builds a model based on convolutions and self-attention  Convolution to model local interactions and self-attention to model global interactions 
BERT: devlin2018bert treats NER as a tagging task 
XLNet: xlnet2019 proposes a generalized autoregressive pretraining method that enables learning bidirectional contexts 
Experiments ::: Machine Reading Comprehension ::: Results
Table shows the experimental results for MRC tasks  With either BERT or XLNet, our proposed DSC loss obtains significant performance boost on both EM and F1  For SQuADv1 1, our proposed method outperforms XLNet by +1 25 in terms of F1 score and +0 84 in terms of EM and achieves 87 65 on EM and 89 51 on F1 for SQuAD v2 0  Moreover, on QuoRef, the proposed method surpasses XLNet results by +1 46 on EM and +1 41 on F1  Another observation is that, XLNet outperforms BERT by a huge margin, and the proposed DSC loss can obtain further performance improvement by an average score above 1 0 in terms of both EM and F1, which indicates the DSC loss is complementary to the model structures 
Experiments ::: Paraphrase Identification
Paraphrases are textual expressions that have the same semantic meaning using different surface words  Paraphrase identification (PI) is the task of identifying whether two sentences have the same meaning or not  We use BERT BIBREF11 and XLNet BIBREF43 as backbones and report F1 score for comparison  Hyperparameters are tuned on the development set of each dataset 
Experiments ::: Paraphrase Identification ::: Datasets
We conduct experiments on two widely used datasets for PI task: MRPC BIBREF44 and QQP 
MRPC is a corpus of sentence pairs automatically extracted from online news sources, with human annotations of whether the sentence pairs are semantically equivalent  The MRPC dataset has imbalanced classes (68% positive, 32% for negative) 
QQP is a collection of question pairs from the community question-answering website Quora  The class distribution in QQP is also unbalanced (37% positive, 63% negative) 
Experiments ::: Paraphrase Identification ::: Results
Table shows the results for PI task  We find that replacing the training objective with DSC introduces performance boost for both BERT and XLNet  Using DSC loss improves the F1 score by +0 58 for MRPC and +0 73 for QQP 
Ablation Studies ::: The Effect of Dice Loss on Accuracy-oriented Tasks
We argue that the most commonly used cross-entropy objective is actually accuracy-oriented, whereas the proposed dice loss (DL) performs as a hard version of F1-score  To explore the effect of the dice loss on accuracy-oriented tasks such as text classification, we conduct experiments on the Stanford Sentiment Treebank sentiment classification datasets including SST-2 and SST-5  We fine-tune BERT$_\text{Large}$ with different training objectives  Experiment results for SST are shown in   For SST-5, BERT with CE achieves 55 57 in terms of accuracy, with DL and DSC losses slightly degrade the accuracy performance and achieve 54 63 and 55 19, respectively  For SST-2, BERT with CE achieves 94 9 in terms of accuracy  The same as SST-5, we observe a slight performance drop with DL and DSC, which means that the dice loss actually works well for F1 but not for accuracy 
Ablation Studies ::: The Effect of Hyperparameters in Tversky index
As mentioned in Section SECREF10, Tversky index (TI) offers the flexibility in controlling the tradeoff between false-negatives and false-positives  In this subsection, we explore the effect of hyperparameters (i e , $\alpha $ and $\beta $) in TI to test how they manipulate the tradeoff  We conduct experiments on the Chinese OntoNotes4 0 NER dataset and English QuoRef MRC dataset to examine the influence of tradeoff between precision and recall  Experiment results are shown in Table   The highest F1 for Chinese OntoNotes4 0 is 84 67 when $\alpha $ is set to 0 6 while for QuoRef, the highest F1 is 68 44 when $\alpha $ is set to 0 4  In addition, we can observe that the performance varies a lot as $\alpha $ changes in distinct datasets, which shows that the hyperparameters $\alpha ,\beta $ play an important role in the proposed method 
Conclusion
In this paper, we alleviate the severe data imbalance issue in NLP tasks  We propose to use dice loss in replacement of the standard cross-entropy loss, which performs as a soft version of F1 score  Using dice loss can help narrow the gap between training objectives and evaluation metrics  Empirically, we show that the proposed training objective leads to significant performance boost for part-of-speech, named entity recognition, machine reading comprehension and paraphrase identification tasks 

ground_truth: One can think $(1-p_{i1})$ as a weight associated with each example, which changes as training proceeds. The intuition of changing $p_{i1}$ to $(1-p_{i1}) p_{i1}$ is to push down the weight of easy examples. For easy examples whose probability are approaching 0 or 1, $(1-p_{i1}) p_{i1}$ makes the model attach significantly less focus to them. Figure FIGREF23 gives gives an explanation from the perspective in derivative: the derivative of $\frac{(1-p)p}{1+(1-p)p}$ with respect to $p$ approaches 0 immediately after $p$ approaches 0, which means the model attends less to examples once they are correctly classified.

associates each training example with a weight in proportion to $(1-p)$, and this weight dynamically changes as training proceeds

prompt_front: You are given a scientific article and a question. Answer the question as concisely as you can, using a single phrase or sentence if possible. If the question cannot be answered based on the information in the article, write "unanswerable". If the question is a yes/no question, answer "yes", "no", or "unanswerable". Do not provide any explanation.

Please answer the questions based on the text provided below. Why masking words in the decoder is helpful?
Context 2: Introduction
Text summarization generates summaries from input documents while keeping salient information  It is an important task and can be applied to several real-world applications  Many methods have been proposed to solve the text summarization problem BIBREF0 , BIBREF1 , BIBREF2 , BIBREF3   There are two main text summarization techniques: extractive and abstractive  Extractive summarization generates summary by selecting salient sentences or phrases from the source text, while abstractive methods paraphrase and restructure sentences to compose the summary  We focus on abstractive summarization in this work as it is more flexible and thus can generate more diverse summaries 
Recently, many abstractive approaches are introduced based on neural sequence-to-sequence framework BIBREF4 , BIBREF0 , BIBREF3 , BIBREF5   Based on the sequence-to-sequence model with copy mechanism BIBREF6 , BIBREF0 incorporates a coverage vector to track and control attention scores on source text  BIBREF4 introduce intra-temporal attention processes in the encoder and decoder to address the repetition and incoherent problem 
There are two issues in previous abstractive methods: 1) these methods use left-context-only decoder, thus do not have complete context when predicting each word  2) they do not utilize the pre-trained contextualized language models on the decoder side, so it is more difficult for the decoder to learn summary representations, context interactions and language modeling together 
Recently, BERT has been successfully used in various natural language processing tasks, such as textual entailment, name entity recognition and machine reading comprehensions  In this paper, we present a novel natural language generation model based on pre-trained language models (we use BERT in this work)  As far as we know, this is the first work to extend BERT to the sequence generation task  To address the above issues of previous abstractive methods, in our model, we design a two-stage decoding process to make good use of BERT's context modeling ability  On the first stage, we generate the summary using a left-context-only-decoder  On the second stage, we mask each word of the summary and predict the refined word one-by-one using a refine decoder  To further improve the naturalness of the generated sequence, we cooperate reinforcement objective with the refine decoder 
The main contributions of this work are:
1  We propose a natural language generation model based on BERT, making good use of the pre-trained language model in the encoder and decoder process, and the model can be trained end-to-end without handcrafted features 
2  We design a two-stage decoder process  In this architecture, our model can generate each word of the summary considering both sides' context information 
3  We conduct experiments on the benchmark datasets CNN/Daily Mail and New York Times  Our model achieves a 33 33 average of ROUGE-1, ROUGE-2 and ROUGE-L on the CNN/Daily Mail, which is state-of-the-art  On the New York Times dataset, our model achieves about 5 6% relative improvement over ROUGE-1 
Text Summarization
In this paper, we focus on single-document multi-sentence summarization and propose a supervised abstractive model based on the neural attentive sequence-to-sequence framework which consists of two parts: a neural network for the encoder and another network for the decoder  The encoder encodes the input sequence to intermediate representation and the decoder predicts one word at a time step given the input sequence representation vector and previous decoded output  The goal of the model is to maximize the probability of generating the correct target sequences  In the encoding and generation process, the attention mechanism is used to concentrate on the most important positions of text  The learning objective of most sequence-to-sequence models is to minimize the negative log likelihood of the generated sequence as following equation shows, where $y^*_i$ is the i-th ground-truth summary token 
$$Loss = - \log \sum _{t=1}^N P(y_t^*|y_{<t}^*, X)$$   (Eq  3)
However, with this objective, traditional sequence generation models consider only one direction context in the decoding process, which could cause performance degradation since complete context of one token contains preceding and following tokens, thus feeding only preceded decoded words to the decoder so that the model may generate unnatural sequences  For example, attentive sequence-to-sequence models often generate sequences with repeated phrases which harm the naturalness  Some previous works mitigate this problem by improving the attention calculation process, but in this paper we show that feeding bi-directional context instead of left-only-context can better alleviate this problem 
Text summarization models are usually classified to abstractive and extractive ones  Recently, extractive models like DeepChannel BIBREF8 , rnn-ext+RL BIBREF9 and NeuSUM BIBREF2 achieve higher performances using well-designed structures  For example, DeepChannel propose a salience estimation network and iteratively extract salient sentences  BIBREF16 train a sentence compression model to teach another latent variable extractive model 
Also, several recent works focus on improving abstractive methods  BIBREF3 design a content selector to over-determine phrases in a source document that should be part of the summary  BIBREF11 introduce inconsistency loss to force words in less attended sentences(which determined by extractive model) to have lower generation probabilities  BIBREF5 extend seq2seq model with an information selection network to generate more informative summaries 
Bi-Directional Pre-Trained Context Encoders
Recently, context encoders such as ELMo, GPT, and BERT have been widely used in many NLP tasks  These models are pre-trained on a huge unlabeled corpus and can generate better contextualized token embeddings, thus the approaches built on top of them can achieve better performance 
Since our method is based on BERT, we illustrate the process briefly here  BERT consists of several layers  In each layer there is first a multi-head self-attention sub-layer and then a linear affine sub-layer with the residual connection  In each self-attention sub-layer the attention scores $e_{ij}$ are first calculated as Eq  ( 5 ) () shows, in which $d_e$ is output dimension, and $W^Q, W^K, W^V$ are parameter matrices 
$$&a_{ij} = \cfrac{(h_iW_Q)(h_jW_K)^T}{\sqrt{d_e}}  \\ &e_{ij} = \cfrac{\exp {e_{ij}}}{\sum _{k=1}^N\exp {e_{ik}}} $$   (Eq  5)
Then the output is calculated as Eq  ( 6 ) shows, which is the weighted sum of previous outputs $h$ added by previous output $h_i$   The last layer outputs is context encoding of input sequence 
$$o_i = h_i + \sum _{j=1}^{N} e_{ij}(h_j W_V) $$   (Eq  6)
Despite the wide usage and huge success, there is also a mismatch problem between these pre-trained context encoders and sequence-to-sequence models  The issue is that while using a pre-trained context encoder like GPT or BERT, they model token-level representations by conditioning on both direction context  During pre-training, they are fed with complete sequences  However, with a left-context-only decoder, these pre-trained language models will suffer from incomplete and inconsistent context and thus cannot generate good enough context-aware word representations, especially during the inference process 
Model
In this section, we describe the structure of our model, which learns to generate an abstractive multi-sentence summary from a given source document 
Based on the sequence-to-sequence framework built on top of BERT, we first design a refine decoder at word-level to tackle the two problems described in the above section  We also introduce a discrete objective for the refine decoders to reduce the exposure bias problem  The overall structure of our model is illustrated in Figure 1  
Problem Formulation
We denote the input document as $X = \lbrace x_1, \ldots , x_m\rbrace $ where $x_i \in \mathcal {X}$ represents one source token  The corresponding summary is denoted as $Y = \lbrace y_1, \ldots , y_L\rbrace $ , $L$ represents the summary length 
Given input document $X$ , we first predict the summary draft by a left-context-only decoder, and then using the generated summary draft we can condition on both context sides and refine the content of the summary  The draft will guide and constrain the refine process of summary 
Summary Draft Generation
The summary draft is based on the sequence-to-sequence model  On the encoder side the input document $X$ is encoded into representation vectors $H = \lbrace h_1, \ldots , h_m\rbrace $ , and then fed to the decoder to generate the summary draft $A = \lbrace a_1, \ldots , a_{|a|}\rbrace $  
We simply use BERT as the encoder  It first maps the input sequence to word embeddings and then computes document embeddings as the encoder's output, denoted by following equation 
$$H = BERT(x_1, \ldots , x_m)$$   (Eq  10)
In the draft decoder, we first introduce BERT's word embedding matrix to map the previous summary draft outputs $\lbrace y_1, \ldots , y_{t-1}\rbrace $ into embeddings vectors $\lbrace q_1, \ldots , q_{t-1}\rbrace $ at t-th time step  Note that as the input sequence of the decoder is not complete, we do not use the BERT network to predict the context vectors here 
Then we introduce an $N$ layer Transformer decoder to learn the conditional probability $P(A|H)$   Transformer's decoder-encoder multi-head attention helps the decoder learn soft alignments between summary and source document  At the t-th time step, the draft decoder predicts output probability conditioned on previous outputs and encoder hidden representations as Eq  ( 13 ) shows, in which $q_{<t} = \lbrace q_1, \ldots , q_{t-1}\rbrace $   Each generated sequence will be truncated in the first position of a special token '[PAD]' 
$$&P^{vocab}_t(w) = f_{dec}(q_{<t}, H)  \\ &L_{dec} = \sum _{i=1}^{|a|} -\log P(a_i = y_i^*|a_{< i}, H) $$   (Eq  13)
As Eq  () shows, the decoder's learning objective is to minimize negative likelihood of conditional probability, in which $y_i^*$ is the i-th ground truth word of summary 
However a decoder with this structure is not sufficient enough: if we use the BERT network in this decoder, then during training and inference, in-complete context(part of sentence) is fed into the BERT module, and although we can fine-tune BERT's parameters, the input distribution is quite different from the pre-train process, and thus harms the quality of generated context representations 
If we just use the embedding matrix here, it will be more difficult for the decoder with fresh parameters to learn to model representations as well as vocabulary probabilities, from a relative small corpus compared to BERT's huge pre-training corpus  In a word, the decoder cannot utilize BERT's ability to generate high quality context vectors, which will also harm performance 
This issue exists when using any other contextualized word representations, so we design a refine process to mitigate it in our approach which will be described in the next sub-section 
As some summary tokens are out-of-vocabulary words and occurs in input document, we incorporate copy mechanism BIBREF6 based on the Transformer decoder, we will describe it briefly 
At decoder time step $t$ , we first calculate the attention probability distribution over source document $X$ using the bi-linear dot product of the last layer decoder output of Transformer $o_t$ and the encoder output $h_j$ , as Eq  ( 15 ) () shows 
$$u_t^j =& o_t W_c h_j \\ \alpha _t^j =& \cfrac{\exp {u_t^j}}{\sum _{k=1}^N\exp {u_t^k}} $$   (Eq  15)
We then calculate copying gate $g_t\in [0, 1]$ , which makes a soft choice between selecting from source and generating from vocabulary, $W_c, W_g, b_g$ are parameters:
$$g_t = sigmoid(W_g \cdot [o_t, h] + b_g) $$   (Eq  16)
Using $g_t$ we calculate the weighted sum of copy probability and generation probability to get the final predicted probability of extended vocabulary $\mathcal {V} + \mathcal {X}$ , where $\mathcal {X}$ is the set of out of vocabulary words from the source document  The final probability is calculated as follow:
$$P_t(w) = (1-g_t)P_t^{vocab}(w) + g_t\sum _{i:w_i=w} \alpha _t^i$$   (Eq  17)
Summary Refine Process
The main reason to introduce the refine process is to enhance the decoder using BERT's contextualized representations, so we do not modify the encoder and reuse it during this process 
On the decoder side, we propose a new word-level refine decoder  The refine decoder receives a generated summary draft as input, and outputs a refined summary  It first masks each word in the summary draft one by one, then feeds the draft to BERT to generate context vectors  Finally it predicts a refined summary word using an $N$ layer Transformer decoder which is the same as the draft decoder  At t-th time step the n-th word of input summary is masked, and the decoder predicts the n-th refined word given other words of the summary 
The learning objective of this process is shown in Eq  ( 19 ), $y_i$ is the i-th summary word and $y_{i}^*$ for the ground-truth summary word, and $a_{\ne i} = \lbrace a_1, \ldots , a_{i-1}, a_{i+1}, \ldots , a_{|y|}\rbrace $  
$$L_{refine} = \sum _{i=1}^{|y|} -\log P(y_i = y_i^*|a_{\ne i}, H) $$   (Eq  19)
From the view of BERT or other contextualized embeddings, the refine decoding process provides a more complete input sequence which is consistent with their pre-training processes  Intuitively, this process works as follows: first the draft decoder writes a summary draft based on a document, and then the refine decoder edits the draft  It concentrates on one word at a time, based on the source document as well as other words 
We design the word-level refine decoder because this process is similar to the cloze task in BERT's pre-train process, therefore by using the ability of the contextual language model the decoder can generate more fluent and natural sequences 
The parameters are shared between the draft decoder and refine decoder, as we find that using individual parameters the model's performance degrades a lot  The reason may be that we use teach-forcing during training, and thus the word-level refine decoder learns to predict words given all the other ground-truth words of summary  This objective is similar to the language model's pre-train objective, and is probably not enough for the decoder to learn to generate refined summaries  So in our model all decoders share the same parameters 
Researchers usually use ROUGE as the evaluation metric for summarization, however during sequence-to-sequence model training, the objective is to maximize the log likelihood of generated sequences  This mis-match harms the model's performance, so we add a discrete objective to the model, and optimize it by introducing the policy gradient method  For example, the discrete objective for the summary draft process is as Eq  ( 21 ) shows, where $a^s$ is the draft summary sampled from predicted distribution, and $R(a^s)$ is the reward score compared with the ground-truth summary, we use ROUGE-L in our experiment  To balance between optimizing the discrete objective and generating readable sequences, we mix the discrete objective with maximum-likelihood objective  As Eq  () shows, minimizing $\hat{L}_{dec}$ is the final objective for the draft process, note here $L_{dec}$ is $-logP(a|x)$   In the refine process we introduce similar objectives 
$$L^{rl}_{dec} = R(a^s)\cdot [-\log (P(a^s|x))]  \\ \hat{L}_{dec} = \gamma * L^{rl}_{dec} + (1 - \gamma ) * L_{dec} $$   (Eq  21)
Learning and Inference
During model training, the objective of our model is sum of the two processes, jointly trained using "teacher-forcing" algorithm  During training we feed the ground-truth summary to each decoder and minimize the objective 
$$L_{model} = \hat{L}_{dec} + \hat{L}_{refine}$$   (Eq  23)
At test time, each time step we choose the predicted word by $\hat{y} = argmax_{y^{\prime }} P(y^{\prime }|x)$ , use beam search to generate the draft summaries, and use greedy search to generate the refined summaries 
Settings
In this work, all of our models are built on $BERT_{BASE}$ , although another larger pre-trained model with better performance ( $BERT_{LARGE}$ ) has published but it costs too much time and GPU memory  We use WordPiece embeddings with a 30,000 vocabulary which is the same as BERT  We set the layer of transformer decoders to 12(8 on NYT50), and set the attention heads number to 12(8 on NYT50), set fully-connected sub-layer hidden size to 3072  We train the model using an Adam optimizer with learning rate of $3e-4$ , $\beta _1=0 9$ , $\beta _2=0 999$ and $\epsilon =10^{-9}$ and use a dynamic learning rate during the training process  For regularization, we use dropout BIBREF13 and label smoothing BIBREF14 in our models and set the dropout rate to 0 15, and the label smoothing value to 0 1  We set the RL objective factor $\gamma $ to 0 99 
During training, we set the batch size to 36, and train for 4 epochs(8 epochs for NYT50 since it has many fewer training samples), after training the best model are selected from last 10 models based on development set performance  Due to GPU memory limit, we use gradient accumulation, set accumulate step to 12 and feed 3 samples at each step  We use beam size 4 and length penalty of 1 0 to generate logical form sequences 
We filter repeated tri-grams in beam-search process by setting word probability to zero if it will generate an tri-gram which exists in the existing summary  It is a nice method to avoid phrase repetition since the two datasets seldom contains repeated tri-grams in one summary  We also fine tune the generated sequences using another two simple rules  When there are multi summary sentences with exactly the same content, we keep the first one and remove the other sentences; we also remove sentences with less than 3 words from the result 
To evaluate the performance of our model, we conduct experiments on CNN/Daily Mail dataset, which is a large collection of news articles and modified for summarization  Following BIBREF0 we choose the non-anonymized version of the dataset, which consists of more than 280,000 training samples and 11490 test set samples 
We also conduct experiments on the New York Times(NYT) dataset which also consists of many news articles  The original dataset can be applied here  In our experiment, we follow the dataset splits and other pre-process settings of BIBREF15   We first filter all samples without a full article text or abstract and then remove all samples with summaries shorter than 50 words  Then we choose the test set based on the date of publication(all examples published after January 1, 2007)  The final dataset contains 22,000 training samples and 3,452 test samples and is called NYT50 since all summaries are longer than 50 words 
We tokenize all sequences of the two datasets using the WordPiece tokenizer  After tokenizing, the average article length and summary length of CNN/Daily Mail are 691 and 51, and NYT50's average article length and summary length are 1152 and 75  We truncate the article length to 512, and the summary length to 100 in our experiment(max summary length is set to 150 on NYT50 as its average golden summary length is longer) 
On CNN/Daily Mail dataset, we report the full-length F-1 score of the ROUGE-1, ROUGE-2 and ROUGE-L metrics, calculated using PyRouge package and the Porter stemmer option  On NYT50, following BIBREF4 we evaluate limited length ROUGE recall score(limit the generated summary length to the ground truth length)  We split NYT50 summaries into sentences by semicolons to calculate the ROUGE scores 
Results and Analysis
Table 1 shows the results on CNN/Daily Mail dataset, we compare the performance of many recent approaches with our model  We classify them to two groups based on whether they are extractive or abstractive models  As the last line of the table shows, the ROUGE-1 and ROUGE-2 score of our full model is comparable with DCA, and outperforms on ROUGE-L  Also, compared to extractive models NeuSUM and MASK- $LM^{global}$ , we achieve slight higher ROUGE-1  Except the four scores, our model outperforms these models on all the other scores, and since we have 95% confidence interval of at most $\pm $ 0 20, these improvements are statistically significant 
As the last four lines of Table 1 show, we conduct an ablation study on our model variants to analyze the importance of each component  We use three ablation models for the experiments  One-Stage: A sequence-to-sequence model with copy mechanism based on BERT; Two-Stage: Adding the word-refine decoder to the One-Stage model; Two-Stage + RL: Full model with refine process cooperated with RL objective 
First, we compare the Two-Stage+RL model with Two-Stage ablation, we observe that the full model outperforms by 0 30 on average ROUGE, suggesting that the reinforcement objective helps the model effectively  Then we analyze the effect of refine process by removing word-level refine from the Two-Stage model, we observe that without the refine process the average ROUGE score drops by 1 69  The ablation study shows that each module is necessary for our full model, and the improvements are statistically significant on all metrics 
To evaluate the impact of summary length on model performance, we compare the average rouge score improvements of our model with different length of ground-truth summaries  As the above sub-figure of Figure 2 shows, compared to Pointer-Generator with Coverage, on length interval 40-80(occupies about 70% of test set) the improvements of our model are higher than shorter samples, confirms that with better context representations, in longer documents our model can achieve higher performance 
As the below sub-figure of Figure 2 shows, compared to extractive baseline: Lead-3 BIBREF0 , the advantage of our model will fall when golden summary length is greater than 80  This probably because that we truncate the long documents and golden summaries and cannot get full information, it could also because that the training data in these intervals is too few to train an abstractive model, so simple extractive method will not fall too far behind 
Additional Results on NYT50
Table 2 shows experiments on the NYT50 corpus  Since the short summary samples are filtered, NYT50 has average longer summaries than CNN/Daily Mail  So the model needs to catch long-term dependency of the sequences to generate good summaries 
The first two lines of Table 2 show results of the two baselines introduced by BIBREF15 : these baselines select first n sentences, or select the first k words from the original document  Also we compare performance of our model with two recent models, we see 2 39 ROUGE-1 improvements compared to the ML+RL with intra-attn approach(previous SOTA) carries over to this dataset, which is a large margin  On ROUGE-2, our model also get an improvement of 0 51  The experiment proves that our approach can outperform competitive methods on different data distributions 
Pre-trained language models
Pre-trained word vectors BIBREF17 , BIBREF18 , BIBREF19 have been widely used in many NLP tasks  More recently, pre-trained language models (ELMo, GPT and BERT), have also achieved great success on several NLP problems such as textual entailment, semantic similarity, reading comprehension, and question answering BIBREF20 , BIBREF21 , BIBREF22  
Some recent works also focus on leveraging pre-trained language models in summarization  BIBREF23 pretrain a language model and use it as the sentiment analyser when generating reviews of goods  BIBREF24 train a language model on golden summaries, and then use it on the decoder side to incorporate prior knowledge 
In this work, we use BERT(which is a pre-trained language model using large scale unlabeled data) on the encoder and decoder of a seq2seq model, and by designing a two stage decoding structure we build a competitive model for abstractive text summarization 
Conclusion and Future Work
In this work, we propose a two-stage model based on sequence-to-sequence paradigm  Our model utilize BERT on both encoder and decoder sides, and introduce reinforce objective in learning process  We evaluate our model on two benchmark datasets CNN/Daily Mail and New York Times, the experimental results show that compared to previous systems our approach effectively improves performance 
Although our experiments are conducted on summarization task, our model can be used in most natural language generation tasks, such as machine translation, question generation and paraphrasing  The refine decoder and mixed objective can also be applied on other sequence generation tasks, and we will investigate on them in future work 
Context 3: Introduction
During the first two decades of the 21st century, the sharing and processing of vast amounts of data has become pervasive  This expansion of data sharing and processing capabilities is both a blessing and a curse  Data helps build better information systems for the digital era and enables further research for advanced data management that benefits the society in general  But the use of this very data containing sensitive information conflicts with private data protection, both from an ethical and a legal perspective 
There are several application domains on which this situation is particularly acute  This is the case of the medical domain BIBREF0  There are plenty of potential applications for advanced medical data management that can only be researched and developed using real data; yet, the use of medical data is severely limited –when not entirely prohibited– due to data privacy protection policies 
One way of circumventing this problem is to anonymise the data by removing, replacing or obfuscating the personal information mentioned, as exemplified in Table TABREF1  This task can be done by hand, having people read and anonymise the documents one by one  Despite being a reliable and simple solution, this approach is tedious, expensive, time consuming and difficult to scale to the potentially thousands or millions of documents that need to be anonymised 
For this reason, numerous of systems and approaches have been developed during the last decades to attempt to automate the anonymisation of sensitive content, starting with the automatic detection and classification of sensitive information  Some of these systems rely on rules, patterns and dictionaries, while others use more advanced techniques related to machine learning and, more recently, deep learning 
Given that this paper is concerned with text documents (e g  medical records), the involved techniques are related to Natural Language Processing (NLP)  When using NLP approaches, it is common to pose the problem of document anonymisation as a sequence labelling problem, i e  classifying each token within a sequence as being sensitive information or not  Further, depending on the objective of the anonymisation task, it is also important to determine the type of sensitive information (names of individuals, addresses, age, sex, etc ) 
The anonymisation systems based on NLP techniques perform reasonably well, but are far from perfect  Depending on the difficulty posed by each dataset or the amount of available data for training machine learning models, the performance achieved by these methods is not enough to fully rely on them in certain situations BIBREF0  However, in the last two years, the NLP community has reached an important milestone thanks to the appearance of the so-called Transformers neural network architectures BIBREF1  In this paper, we conduct several experiments in sensitive information detection and classification on Spanish clinical text using BERT (from `Bidirectional Encoder Representations from Transformers') BIBREF2 as the base for a sequence labelling approach  The experiments are carried out on two datasets: the MEDDOCAN: Medical Document Anonymization shared task dataset BIBREF3, and NUBes BIBREF4, a corpus of real medical reports in Spanish  In these experiments, we compare the performance of BERT with other machine-learning-based systems, some of which use language-specific features  Our aim is to evaluate how good a BERT-based model performs without language nor domain specialisation apart from the training data labelled for the task at hand 
The rest of the paper is structured as follows: the next section describes related work about data anonymisation in general and clinical data anonymisation in particular; it also provides a more detailed explanation and background about the Transformers architecture and BERT  Section SECREF3 describes the data involved in the experiments and the systems evaluated in this paper, including the BERT-based system; finally, it details the experimental design  Section SECREF4 introduces the results for each set of experiments  Finally, Section SECREF5 contains the conclusions and future lines of work 
Related Work
The state of the art in the field of Natural Language Processing (NLP) has reached an important milestone in the last couple of years thanks to deep-learning architectures, increasing in several points the performance of new models for almost any text processing task 
The major change started with the Transformers model proposed by vaswani2017attention  It substituted the widely used recurrent and convolutional neural network architectures by another approach based solely on self-attention, obtaining an impressive performance gain  The original proposal was focused on an encoder-decoder architecture for machine translation, but soon the use of Transformers was made more general BIBREF1  There are several other popular models that use Transformers, such as Open AI's GPT and GPT2 BIBREF5, RoBERTa BIBREF6 and the most recent XLNet BIBREF7; still, BERT BIBREF2 is one of the most widespread Transformer-based models 
BERT trains its unsupervised language model using a Masked Language Model and Next Sentence Prediction  A common problem in NLP is the lack of enough training data  BERT can be pre-trained to learn general or specific language models using very large amounts of unlabelled text (e g  web content, Wikipedia, etc ), and this knowledge can be transferred to a different downstream task in a process that receives the name fine-tuning 
devlin2018bert have used fine-tuning to achieve state-of-the-art results on a wide variety of challenging natural language tasks, such as text classification, Question Answering (QA) and Named Entity Recognition and Classification (NERC)  BERT has also been used successfully by other community practitioners for a wide range of NLP-related tasks BIBREF8, BIBREF9 
Regarding the task of data anonymisation in particular, anonymisation systems may follow different approaches and pursue different objectives (Cormode and Srivastava, 2009)  The first objective of these systems is to detect and classify the sensitive information contained in the documents to be anonymised  In order to achieve that, they use rule-based approaches, Machine Learning (ML) approaches, or a combination of both 
Although most of these efforts are for English texts –see, among others, the i2b2 de-identification challenges BIBREF10, BIBREF11, dernon2016deep, or khin2018deep–, other languages are also attracting growing interest  Some examples are mamede2016automated for Portuguese and tveit2004anonymization for Norwegian  With respect to the anonymisation of text written in Spanish, recent studies include medina2018building, hassan2018anonimizacion and garcia2018automating  Most notably, in 2019 the first community challenge about anonymisation of medical documents in Spanish, MEDDOCAN BIBREF3, was held as part of the IberLEF initiative  The winners of the challenge –the Neither-Language-nor-Domain-Experts (NLNDE) BIBREF12– achieved F1-scores as high as 0 975 in the task of sensitive information detection and categorisation by using recurrent neural networks with Conditional Random Field (CRF) output layers 
At the same challenge, mao2019hadoken occupied the 8th position among 18 participants using BERT  According to the description of the system, the authors used BERT-Base Multilingual Cased and an output CRF layer  However, their system is $\sim $3 F1-score points below our implementation without the CRF layer 
Materials and Methods
The aim of this paper is to evaluate BERT's multilingual model and compare it to other established machine-learning algorithms in a specific task: sensitive data detection and classification in Spanish clinical free text  This section describes the data involved in the experiments and the systems evaluated  Finally, we introduce the experimental setup 
Materials and Methods ::: Data
Two datasets are exploited in this article  Both datasets consist of plain text containing clinical narrative written in Spanish, and their respective manual annotations of sensitive information in BRAT BIBREF13 standoff format  In order to feed the data to the different algorithms presented in Section SECREF7, these datasets were transformed to comply with the commonly used BIO sequence representation scheme BIBREF14 
Materials and Methods ::: Data ::: NUBes-PHI
NUBes BIBREF4 is a corpus of around 7,000 real medical reports written in Spanish and annotated with negation and uncertainty information  Before being published, sensitive information had to be manually annotated and replaced for the corpus to be safely shared  In this article, we work with the NUBes version prior to its anonymisation, that is, with the manual annotations of sensitive information  It follows that the version we work with is not publicly available and, due to contractual restrictions, we cannot reveal the provenance of the data  In order to avoid confusion between the two corpus versions, we henceforth refer to the version relevant in this paper as NUBes-PHI (from `NUBes with Personal Health Information') 
NUBes-PHI consists of 32,055 sentences annotated for 11 different sensitive information categories  Overall, it contains 7,818 annotations  The corpus has been randomly split into train (72%), development (8%) and test (20%) sets to conduct the experiments described in this paper  The size of each split and the distribution of the annotations can be consulted in Tables and , respectively 
The majority of sensitive information in NUBes-PHI are temporal expressions (`Date' and `Time'), followed by healthcare facility mentions (`Hospital'), and the age of the patient  Mentions of people are not that frequent, with physician names (`Doctor') occurring much more often than patient names (`Patient')  The least frequent sensitive information types, which account for $\sim $10% of the remaining annotations, consist of the patient's sex, job, and kinship, and locations other than healthcare facilities (`Location')  Finally, the tag `Other' includes, for instance, mentions to institutions unrelated to healthcare and whether the patient is right- or left-handed  It occurs just 36 times 
Materials and Methods ::: Data ::: The MEDDOCAN corpus
The organisers of the MEDDOCAN shared task BIBREF3 curated a synthetic corpus of clinical cases enriched with sensitive information by health documentalists  In this regard, the MEDDOCAN evaluation scenario could be said to be somewhat far from the real use case the technology developed for the shared task is supposed to be applied in  However, at the moment it also provides the only public means for a rigorous comparison between systems for sensitive health information detection in Spanish texts 
The size of the MEDDOCAN corpus is shown in Table   Compared to NUBes-PHI (Table ), this corpus contains more sensitive information annotations, both in absolute and relative terms 
The sensitive annotation categories considered in MEDDOCAN differ in part from those in NUBes-PHI  Most notably, it contains finer-grained labels for location-related mentions –namely, `Address', `Territory', and `Country'–, and other sensitive information categories that we did not encounter in NUBes-PHI (e g , identifiers, phone numbers, e-mail addresses, etc )  In total, the MEDDOCAN corpus has 21 sensitive information categories  We refer the reader to the organisers' article BIBREF3 for more detailed information about this corpus 
Materials and Methods ::: Systems
Apart from experimenting with a pre-trained BERT model, we have run experiments with other systems and baselines, to compare them and obtain a better perspective about BERT's performance in these datasets 
Materials and Methods ::: Systems ::: Baseline
As the simplest baseline, a sensitive data recogniser and classifier has been developed that consists of regular-expressions and dictionary look-ups  For each category to detect a specific method has been implemented  For instance, the Date, Age, Time and Doctor detectors are based on regular-expressions; Hospital, Sex, Kinship, Location, Patient and Job are looked up in dictionaries  The dictionaries are hand-crafted from the training data available, except for the Patient's case, for which the possible candidates considered are the 100 most common female and male names in Spain according to the Instituto Nacional de Estadística (INE; Spanish Statistical Office) 
Materials and Methods ::: Systems ::: CRF
Conditional Random Fields (CRF) BIBREF15 have been extensively used for tasks of sequential nature  In this paper, we propose as one of the competitive baselines a CRF classifier trained with sklearn-crfsuite for Python 3 5 and the following configuration: algorithm = lbfgs; maximum iterations = 100; c1 = c2 = 0 1; all transitions = true; optimise = false  The features extracted from each token are as follows:
[noitemsep]
prefixes and suffixes of 2 and 3 characters;
the length of the token in characters and the length of the sentence in tokens;
whether the token is all-letters, a number, or a sequence of punctuation marks;
whether the token contains the character `@';
whether the token is the start or end of the sentence;
the token's casing and the ratio of uppercase characters, digits, and punctuation marks to its length;
and, the lemma, part-of-speech tag, and named-entity tag given by ixa-pipes BIBREF16 upon analysing the sentence the token belongs to 
Noticeably, none of the features used to train the CRF classifier is domain-dependent  However, the latter group of features is language dependent 
Materials and Methods ::: Systems ::: spaCy
spaCy is a widely used NLP library that implements state-of-the-art text processing pipelines, including a sequence-labelling pipeline similar to the one described by strubell2017fast  spaCy offers several pre-trained models in Spanish, which perform basic NLP tasks such as Named Entity Recognition (NER)  In this paper, we have trained a new NER model to detect NUBes-PHI labels  For this purpose, the new model uses all the labels of the training corpus coded with its context at sentence level  The network optimisation parameters and dropout values are the ones recommended in the documentation for small datasets  Finally, the model is trained using batches of size 64  No more features are included, so the classifier is language-dependent but not domain-dependent 
Materials and Methods ::: Systems ::: BERT
As introduced earlier, BERT has shown an outstanding performance in NERC-like tasks, improving the start-of-the-art results for almost every dataset and language  We take the same approach here, by using the model BERT-Base Multilingual Cased with a Fully Connected (FC) layer on top to perform a fine-tuning of the whole model for an anonymisation task in Spanish clinical data  Our implementation is built on PyTorch and the PyTorch-Transformers library BIBREF1  The training phase consists in the following steps (roughly depicted in Figure ):
Pre-processing: since we are relying on a pre-trained BERT model, we must match the same configuration by using a specific tokenisation and vocabulary  BERT also needs that the inputs contains special tokens to signal the beginning and the end of each sequence 
Fine-tuning: the pre-processed sequence is fed into the model  BERT outputs the contextual embeddings that encode each of the inputted tokens

ground_truth: ecause this process is similar to the cloze task in BERT's pre-train process, therefore by using the ability of the contextual language model the decoder can generate more fluent and natural sequences.

prompt_front: You are given a scientific article and a question. Answer the question as concisely as you can, using a single phrase or sentence if possible. If the question cannot be answered based on the information in the article, write "unanswerable". If the question is a yes/no question, answer "yes", "no", or "unanswerable". Do not provide any explanation.

Please answer the questions based on the text provided below. What are the clinical datasets used in the paper?
Context 3:  This embedding representation for each token is fed into the FC linear layer after a dropout layer (with a 0 1 dropout probability), which in turn outputs the logits for each possible class  The cross-entropy loss function is calculated comparing the logits and the gold labels, and the error is back-propagated to adjust the model parameters 
We have trained the model using an AdamW optimiser BIBREF17 with the learning rate set to 3e-5, as recommended by devlin2018bert, and with a gradient clipping of 1 0  We also applied a learning-rate scheduler that warms up the learning rate from zero to its maximum value as the training progresses, which is also a common practice  For each experiment set proposed below, the training was run with an early-stopping patience of 15 epochs  Then, the model that performed best against the development set was used to produce the reported results 
The experiments were run on a 64-core server with operating system Ubuntu 16 04, 250GB of RAM memory, and 4 GeForce RTX 2080 GPUs with 11GB of memory  The maximum sequence length was set at 500 and the batch size at 12  In this setting, each epoch –a full pass through all the training data– required about 10 minutes to complete 
Materials and Methods ::: Experimental design
We have conducted experiments with BERT in the two datasets of Spanish clinical narrative presented in Section SECREF3 The first experiment set uses NUBes-PHI, a corpus of real medical reports manually annotated with sensitive information  Because this corpus is not publicly available, and in order to compare the BERT-based model to other related published systems, the second set of experiments uses the MEDDOCAN 2019 shared task competition dataset  The following sections provide greater detail about the two experimental setups 
Materials and Methods ::: Experimental design ::: Experiment A: NUBes-PHI
In this experiment set, we evaluate all the systems presented in Section SECREF7, namely, the rule-based baseline, the CRF classifier, the spaCy entity tagger, and BERT  The evaluation comprises three scenarios of increasing difficulty:
[noitemsep]
- Evaluates the performance of the systems at predicting whether each token is sensitive or non-sensitive; that is, the measurements only take into account whether a sensitive token has been recognised or not, regardless of the BIO label and the category assigned  This scenario shows how good a system would be at obfuscating sensitive data (e g , by replacing sensitive tokens with asterisks) 
- We measure the performance of the systems at predicting the sensitive information type of each token –i e , the 11 categories presented in Section SECREF5 or `out'  Detecting entity types correctly is important if a system is going to be used to replace sensitive data by fake data of the same type (e g , random people names) 
- This is the strictest evaluation, as it takes into account both the BIO label and the category assigned to each individual token  Being able to discern between two contiguous sensitive entities of the same type is relevant not only because it is helpful when producing fake replacements, but because it also yields more accurate statistics of the sensitive information present in a given document collection 
The systems are evaluated in terms of micro-average precision, recall and F1-score in all the scenarios 
In addition to the scenarios proposed, a subject worth being studied is the need of labelled data  Manually labelled data is an scarce and expensive resource, which for some application domains or languages is difficult to come by  In order to obtain an estimation of the dependency of each system on the available amount of training data, we have retrained all the compared models using decreasing amounts of data –from 100% of the available training instances to just 1%  The same data subsets have been used to train all the systems  Due to the knowledge transferred from the pre-trained BERT model, the BERT-based model is expected to be more robust to data scarcity than those that start their training from scratch 
Materials and Methods ::: Experimental design ::: Experiment B: MEDDOCAN
In this experiment set, our BERT implementation is compared to several systems that participated in the MEDDOCAN challenge: a CRF classifier BIBREF18, a spaCy entity recogniser BIBREF18, and NLNDE BIBREF12, the winner of the shared task and current state of the art for sensitive information detection and classification in Spanish clinical text  Specifically, we include the results of a domain-independent NLNDE model (S2), and the results of a model enriched with domain-specific embeddings (S3)  Finally, we include the results obtained by mao2019hadoken with a CRF output layer on top of BERT embeddings  MEDDOCAN consists of two scenarios:
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- This evaluation measures how good a system is at detecting sensitive text spans, regardless of the category assigned to them 
- In this scenario, systems are required to match exactly not only the boundaries of each sensitive span, but also the category assigned 
The systems are evaluated in terms of micro-averaged precision, recall and F-1 score  Note that, in contrast to the evaluation in Experiment A, MEDDOCAN measurements are entity-based instead of tokenwise  An exhaustive explanation of the MEDDOCAN evaluation procedure is available online, as well as the official evaluation script, which we used to obtain the reported results 
Results
This section describes the results obtained in the two sets of experiments: NUBes-PHI and MEDDOCAN 
Results ::: Experiment A: NUBes-PHI
Table shows the results of the conducted experiments in NUBes-PHI for all the compared systems  The included baseline serves to give a quick insight about how challenging the data is  With simple regular expressions and gazetteers a precision of 0 853 is obtained  On the other hand, the recall, which directly depends on the coverage provided by the rules and resources, drops to 0 469  Hence, this task is unlikely to be solved without the generalisation capabilities provided by machine-learning and deep-learning models 
Regarding the detection scenario –that is, the scenario concerned with a binary classification to determine whether each individual token conveys sensitive information or not–, it can be observed that BERT outperforms its competitors  A fact worth highlighting is that, according to these results, BERT achieves a precision lower than the rest of the systems (i e , it makes more false positive predictions); in exchange, it obtains a remarkably higher recall  Noticeably, it reaches a recall of 0 979, improving by more than 4 points the second-best system, spaCy 
The table also shows the results for the relaxed metric that only takes into account the entity type detected, regardless of the BIO label (i e , ignoring whether the token is at the beginning or in the middle of a sensitive sequence of tokens)  The conclusions are very similar to those extracted previously, with BERT gaining 2 1 points of F1-score over the CRF based approach  The confusion matrices of the predictions made by CRF, spaCy, and BERT in this scenario are shown in Table   As can bee seen, BERT has less difficulty in predicting correctly less frequent categories, such as `Location', `Job', and `Patient'  One of the most common mistakes according to the confusion matrices is classifying hospital names as `Location' instead of the more accurate `Hospital'; this is hardly a harmful error, given that a hospital is actually a location  Last, the category `Other' is completely leaked by all the compared systems, most likely due to its almost total lack of support in both training and evaluation datasets 
To finish with this experiment set, Table also shows the strict classification precision, recall and F1-score for the compared systems  Despite the fact that, in general, the systems obtain high values, BERT outperforms them again  BERT's F1-score is 1 9 points higher than the next most competitive result in the comparison  More remarkably, the recall obtained by BERT is about 5 points above 
Upon manual inspection of the errors committed by the BERT-based model, we discovered that it has a slight tendency towards producing ill-formed BIO sequences (e g, starting a sensitive span with `Inside' instead of `Begin'; see Table )  We could expect that complementing the BERT-based model with a CRF layer on top would help enforce the emission of valid sequences, alleviating this kind of errors and further improving its results 
Finally, Figure shows the impact of decreasing the amount of training data in the detection scenario  It shows the difference in precision, recall, and F1-score with respect to that obtained using 100% of the training data  A general downward trend can be observed, as one would expect: less training data leads to less accurate predictions  However, the BERT-based model is the most robust to training-data reduction, showing an steadily low performance loss  With 1% of the dataset (230 training instances), the BERT-based model only suffers a striking 7-point F1-score loss, in contrast to the 32 and 39 points lost by the CRF and spaCy models, respectively  This steep performance drop stems to a larger extent from recall decline, which is not that marked in the case of BERT  Overall, these results indicate that the transfer-learning achieved through the BERT multilingual pre-trained model not only helps obtain better results, but also lowers the need of manually labelled data for this application domain 
Results ::: Experiment B: MEDDOCAN
The results of the two MEDDOCAN scenarios –detection and classification– are shown in Table   These results follow the same pattern as in the previous experiments, with the CRF classifier being the most precise of all, and BERT outperforming both the CRF and spaCy classifiers thanks to its greater recall  We also show the results of mao2019hadoken who, despite of having used a BERT-based system, achieve lower scores than our models  The reason why it should be so remain unclear 
With regard to the winner of the MEDDOCAN shared task, the BERT-based model has not improved the scores obtained by neither the domain-dependent (S3) nor the domain-independent (S2) NLNDE model  However, attending to the obtained results, BERT remains only 0 3 F1-score points behind, and would have achieved the second position among all the MEDDOCAN shared task competitors  Taking into account that only 3% of the gold labels remain incorrectly annotated, the task can be considered almost solved, and it is not clear if the differences among the systems are actually significant, or whether they stem from minor variations in initialisation or a long-tail of minor labelling inconsistencies 
Conclusions and Future Work
In this work we have briefly introduced the problems related to data privacy protection in clinical domain  We have also described some of the groundbreaking advances on the Natural Language Processing field due to the appearance of Transformers-based deep-learning architectures and transfer learning from very large general-domain multilingual corpora, focusing our attention in one of its most representative examples, Google's BERT model 
In order to assess the performance of BERT for Spanish clinical data anonymisation, we have conducted several experiments with a BERT-based sequence labelling approach using the pre-trained multilingual BERT model shared by Google as the starting point for the model training  We have compared this BERT-based sequence labelling against other methods and systems  One of the experiments uses the MEDDOCAN 2019 shared task dataset, while the other uses a novel Spanish clinical reports dataset called NUBes-PHI 
The results of the experiments show that, in NUBes-PHI, the BERT-based model outperforms the other systems without requiring any adaptation or domain-specific feature engineering, just by being trained on the provided labelled data  Interestingly, the BERT-based model obtains a remarkably higher recall than the other systems  High recall is a desirable outcome because, when anonymising sensible documents, the accidental leak of sensible data is likely to be more dangerous than the unintended over-obfuscation of non-sensitive text 
Further, we have conducted an additional experiment on this dataset by progressively reducing the training data for all the compared systems  The BERT-based model shows the highest robustness to training-data scarcity, loosing only 7 points of F1-score when trained on 230 instances instead of 21,371  These observation are in line with the results obtained by the NLP community using BERT for other tasks 
The experiments with the MEDDOCAN 2019 shared task dataset follow the same pattern  In this case, the BERT-based model falls 0 3 F1-score points behind the shared task winning system, but it would have achieved the second position in the competition with no further refinement 
Since we have used a pre-trained multilingual BERT model, the same approach is likely to work for other languages just by providing some labelled training data  Further, this is the simplest fine-tuning that can be performed based on BERT  More sophisticated fine-tuning layers could help improve the results  For example, it could be expected that a CRF layer helped enforce better BIO tagging sequence predictions  Precisely, mao2019hadoken participated in the MEDDOCAN competition using a BERT+CRF architecture, but their reported scores are about 3 points lower than our implementation  From the description of their work, it is unclear what the source of this score difference could be 
Further, at the time of writing this paper, new multilingual pre-trained models and Transformer architectures have become available  It would not come as a surprise that these new resources and systems –e g , XLM-RoBERTa BIBREF19 or BETO BIBREF20, a BERT model fully pre-trained on Spanish texts– further advanced the state of the art in this task 
Acknowledgements
This work has been supported by Vicomtech and partially funded by the project DeepReading (RTI2018-096846-B-C21, MCIU/AEI/FEDER,UE) 

ground_truth: MEDDOCAN, NUBes-PHI

MEDDOCAN, NUBes