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. Which toolkits do they use?
Context 1: Introduction
As social media, specially Twitter, takes on an influential role in presidential elections in the U S , natural language processing of political tweets BIBREF0 has the potential to help with nowcasting and forecasting of election results as well as identifying the main issues with a candidate – tasks of much interest to journalists, political scientists, and campaign organizers BIBREF1  As a methodology to obtain training data for a machine learning system that analyzes political tweets, BIBREF2 devised a crowdsourcing scheme with variable crowdworker numbers based on the difficulty of the annotation task  They provided a dataset of tweets where the sentiments towards political candidates were labeled both by experts in political communication and by crowdworkers who were likely not domain experts  BIBREF2 revealed that crowdworkers can match expert performance relatively accurately and in a budget-efficient manner  Given this result, the authors envisioned future work in which groundtruth labels would be crowdsourced for a large number of tweets and then used to design an automated NLP tool for political tweet analysis 
The question we address here is: How accurate are existing NLP tools for political tweet analysis? These tools would provide a baseline performance that any new machine learning system for political tweet analysis would compete against  We here explore whether existing NLP systems can answer the questions "What sentiment?" and "Towards whom?" accurately for the dataset of political tweets provided by BIBREF2  In our analysis, we include NLP tools with publicly-available APIs, even if the tools were not specifically designed for short texts like tweets, and, in particular, political tweets 
Our experiments reveal that the task of entity-level sentiment analysis is difficult for existing tools to answer accurately while the recognition of the entity, here, which politician, was easier 
NLP Toolkits
NLP toolkits typically have the following capabilities: tokenization, part-of-speech (PoS) tagging, chunking, named entity recognition and sentiment analysis  In a study by BIBREF3, it is shown that the well-known NLP toolkits NLTK BIBREF4, Stanford CoreNLP BIBREF5, and TwitterNLP BIBREF6 have tokenization, PoS tagging and NER modules in their pipelines  There are two main approaches for NER: (1) rule-based and (2) statistical or machine learning based  The most ubiquitous algorithms for sequence tagging use Hidden Markov Models BIBREF7, Maximum Entropy Markov Models BIBREF7, BIBREF8, or Conditional Random Fields BIBREF9  Recent works BIBREF10, BIBREF11 have used recurrent neural networks with attention modules for NER 
Sentiment detection tools like SentiStrength BIBREF12 and TensiStrength BIBREF13 are rule-based tools, relying on various dictionaries of emoticons, slangs, idioms, and ironic phrases, and set of rules that can detect the sentiment of a sentence overall or a targeted sentiment  Given a list of keywords, TensiStrength (similar to SentiStrength) reports the sentiment towards selected entities in a sentence, based on five levels of relaxation and five levels of stress 
Among commercial NLP toolkits (e g , BIBREF14, BIBREF15, BIBREF16), we selected BIBREF17 and BIBREF18 for our experiments, which, to the best of our knowledge, are the only publicly accessible commercial APIs for the task of entity-level sentiment analysis that is agnostic to the text domain  We also report results of TensiStrength BIBREF13, TwitterNLP BIBREF6, BIBREF19, CogComp-NLP BIBREF20, and Stanford NLP NER BIBREF21 
Dataset and Analysis Methodology
We used the 1,000-tweet dataset by BIBREF2 that contains the named-entities labels and entity-level sentiments for each of the four 2016 presidential primary candidates Bernie Sanders, Donald Trump, Hillary Clinton, and Ted Cruz, provided by crowdworkers, and by experts in political communication, whose labels are considered groundtruth  The crowdworkers were located in the US and hired on the BIBREF22 platform  For the task of entity-level sentiment analysis, a 3-scale rating of "negative," "neutral," and "positive" was used by the annotators 
BIBREF2 proposed a decision tree approach for computing the number of crowdworkers who should analyze a tweet based on the difficulty of the task  Tweets are labeled by 2, 3, 5, or 7 workers based on the difficulty of the task and the level of disagreement between the crowdworkers  The model computes the number of workers based on how long a tweet is, the presence of a link in a tweet, and the number of present sarcasm signals  Sarcasm is often used in political tweets and causes disagreement between the crowdworkers  The tweets that are deemed to be sarcastic by the decision tree model, are expected to be more difficult to annotate, and hence are allocated more crowdworkers to work on 
We conducted two sets of experiments  In the first set, we used BIBREF23, BIBREF17, and BIBREF18, for entity-level sentiment analysis; in the second set, BIBREF17, BIBREF19, BIBREF24, BIBREF25, and BIBREF26, BIBREF18 for named-entity recognition 
In the experiments that we conducted with TwitterNLP for named-entity recognition, we worked with the default values of the model  Furthermore, we selected the 3-class Stanford NER model, which uses the classes “person,” “organization,” and “location” because it resulted in higher accuracy compared to the 7-class model  For CogComp-NLP NER we used Ontonotes 5 0 NER model BIBREF27  For spaCy NER we used the `en_core_web_lg' model 
We report the experimental results for our two tasks in terms of the correct classification rate (CCR)  For sentiment analysis, we have a three-class problem (positive, negative, and neutral), where the classes are mutually exclusive  The CCR, averaged for a set of tweets, is defined to be the number of correctly-predicted sentiments over the number of groundtruth sentiments in these tweets  For NER, we consider that each tweet may reference up to four candidates, i e , targeted entities  The CCR, averaged for a set of tweets, is the number of correctly predicted entities (candidates) over the number of groundtruth entities (candidates) in this set 
Results and Discussion
The dataset of 1,000 randomly selected tweets contains more than twice as many tweets about Trump than about the other candidates  In the named-entity recognition experiment, the average CCR of crowdworkers was 98 6%, while the CCR of the automated systems ranged from 77 2% to 96 7%  For four of the automated systems, detecting the entity Trump was more difficult than the other entities (e g , spaCy 72 7% for the entity Trump vs  above 91% for the other entities)  An example of incorrect NER is shown in Figure FIGREF1 top  The difficulties the automated tools had in NER may be explained by the fact that the tools were not trained on tweets, except for TwitterNLP, which was not in active development when the data was created BIBREF1 
In the sentiment analysis experiments, we found that a tweet may contain multiple sentiments  The groundtruth labels contain 210 positive sentiments, 521 neutral sentiments, and 305 negative sentiments to the candidates  We measured the CCR, across all tweets, to be 31 7% for Rosette Text Analytics, 43 2% for Google Cloud, 44 2% for TensiStrength, and 74 7% for the crowdworkers  This means the difference between the performance of the tools and the crowdworkers is significant – more than 30 percent points 
Crowdworkers correctly identified 62% of the neutral, 85% of the positive, and 92% of the negative sentiments  Google Cloud correctly identified 88% of the neutral sentiments, but only 3% of the positive, and 19% of the negative sentiments  TensiStrength correctly identified 87 2% of the neutral sentiments, but 10 5% of the positive, and 8 1% of the negative sentiments  Rosette Text Analytics correctly identified 22 7% of neutral sentiments, 38 1% of negative sentiments and 40 9% of positive sentiments  The lowest and highest CCR pertains to tweets about Trump and Sanders for both Google Cloud and TensiStrength, Trump and Clinton for Rosette Text Analytics, and Clinton and Cruz for crowdworkers  An example of incorrect ELS analysis is shown in Figure FIGREF1 bottom 
Conclusions and Future Work
Our results show that existing NLP systems cannot accurately perform sentiment analysis of political tweets in the dataset we experimented with  Labeling by humans, even non-expert crowdworkers, yields accuracy results that are well above the results of existing automated NLP systems  In future work we will therefore use a crowdworker-labeled dataset to train a new machine-learning based NLP system for tweet analysis  We will ensure that the training data is balanced among classes  Our plan is to use state-of-the-art deep neural networks and compare their performance for entity-level sentiment analysis of political tweets 
Acknowledgments
Partial support of this work by the Hariri Institute for Computing and Computational Science & Engineering at Boston University (to L G ) and a Google Faculty Research Award (to M B  and L G ) is gratefully acknowledged  Additionally, we would like to thank Daniel Khashabi for his help in running the CogComp-NLP Python API and Mike Thelwal for his help with TensiStrength  We are also grateful to the Stanford NLP group for clarifying some of the questions we had with regards to the Stanford NER tool 
Context 2: Introduction
Bidirectional Encoder Representations from Transformers (BERT) is a novel Transformer BIBREF0 model, which recently achieved state-of-the-art performance in several language understanding tasks, such as question answering, natural language inference, semantic similarity, sentiment analysis, and others BIBREF1  While well-suited to dealing with relatively short sequences, Transformers suffer from a major issue that hinders their applicability in classification of long sequences, i e  they are able to consume only a limited context of symbols as their input BIBREF2 
There are several natural language (NLP) processing tasks that involve such long sequences  Of particular interest are topic identification of spoken conversations BIBREF3, BIBREF4, BIBREF5 and call center customer satisfaction prediction BIBREF6, BIBREF7, BIBREF8, BIBREF9  Call center conversations, while usually quite short and to the point, often involve agents trying to solve very complex issues that the customers experience, resulting in some calls taking even an hour or more  For speech analytics purposes, these calls are typically transcribed using an automatic speech recognition (ASR) system, and processed in textual representations further down the NLP pipeline  These transcripts sometimes exceed the length of 5000 words  Furthermore, temporal information might play an important role in tasks like CSAT  For example, a customer may be angry at the beginning of the call, but after her issue is resolved, she would be very satisfied with the way it was handled  Therefore, simple bag of words models, or any model that does not include temporal dependencies between the inputs, may not be well-suited to handle this category of tasks  This motivates us to employ model such as BERT in this task 
In this paper, we propose a method that builds upon BERT's architecture  We split the input text sequence into shorter segments in order to obtain a representation for each of them using BERT  Then, we use either a recurrent LSTM BIBREF10 network, or another Transformer, to perform the actual classification  We call these techniques Recurrence over BERT (RoBERT) and Transformer over BERT (ToBERT)  Given that these models introduce a hierarchy of representations (segment-wise and document-wise), we refer to them as Hierarchical Transformers  To the best of our knowledge, no attempt has been done before to use the Transformer architecture for classification of such long sequences 
Our novel contributions are:
Two extensions - RoBERT and ToBERT - to the BERT model, which enable its application in classification of long texts by performing segmentation and using another layer on top of the segment representations 
State-of-the-art results on the Fisher topic classification task 
Significant improvement on the CSAT prediction task over the MS-CNN model 
Related work
Several dimensionality reduction algorithms such as RBM, autoencoders, subspace multinomial models (SMM) are used to obtain a low dimensional representation of documents from a simple BOW representation and then classify it using a simple linear classifiers BIBREF11, BIBREF12, BIBREF13, BIBREF4  In BIBREF14 hierarchical attention networks are used for document classification  They evaluate their model on several datasets with average number of words around 150  Character-level CNN are explored in BIBREF15 but it is prohibitive for very long documents  In BIBREF16, dataset collected from arXiv papers is used for classification  For classification, they sample random blocks of words and use them together for classification instead of using full document which may work well as arXiv papers are usually coherent and well written on a well defined topic  Their method may not work well on spoken conversations as random block of words usually do not represent topic of full conversation 
Several researchers addressed the problem of predicting customer satisfaction BIBREF6, BIBREF7, BIBREF8, BIBREF9  In most of these works, logistic regression, SVM, CNN are applied on different kinds of representations 
In BIBREF17, authors use BERT for document classification but the average document length is less than BERT maximum length 512  TransformerXL BIBREF2 is an extension to the Transformer architecture that allows it to better deal with long inputs for the language modelling task  It relies on the auto-regressive property of the model, which is not the case in our tasks 
Method ::: BERT
Because our work builds heavily upon BERT, we provide a brief summary of its features  BERT is built upon the Transformer architecture BIBREF0, which uses self-attention, feed-forward layers, residual connections and layer normalization as the main building blocks  It has two pre-training objectives:
Masked language modelling - some of the words in a sentence are being masked and the model has to predict them based on the context (note the difference from the typical autoregressive language model training objective);
Next sentence prediction - given two input sequences, decide whether the second one is the next sentence or not 
BERT has been shown to beat the state-of-the-art performance on 11 tasks with no modifications to the model architecture, besides adding a task-specific output layer BIBREF1  We follow same procedure suggested in BIBREF1 for our tasks  Fig  FIGREF8 shows the BERT model for classification  We obtain two kinds of representation from BERT: pooled output from last transformer block, denoted by H, and posterior probabilities, denoted by P  There are two variants of BERT - BERT-Base and BERT-Large  In this work we are using BERT-Base for faster training and experimentation, however, our methods are applicable to BERT-Large as well  BERT-Base and BERT-Large are different in model parameters such as number of transformer blocks, number of self-attention heads  Total number of parameters in BERT-Base are 110M and 340M in BERT-Large 
BERT suffers from major limitations in terms of handling long sequences  Firstly, the self-attention layer has a quadratic complexity $O(n^2)$ in terms of the sequence length $n$ BIBREF0  Secondly, BERT uses a learned positional embeddings scheme BIBREF1, which means that it won't likely be able to generalize to positions beyond those seen in the training data 
To investigate the effect of fine-tuning BERT on task performance, we use either the pre-trained BERT weights, or the weights from a BERT fine-tuned on the task-specific dataset on a segment-level (i e  we preserve the original label but fine-tune on each segment separately instead of on the whole text sequence)  We compare these results to using the fine-tuned segment-level BERT predictions directly as inputs to the next layer 
Method ::: Recurrence over BERT
Given that BERT is limited to a particular input length, we split the input sequence into segments of a fixed size with overlap  For each of these segments, we obtain H or P from BERT model  We then stack these segment-level representations into a sequence, which serves as input to a small (100-dimensional) LSTM layer  Its output serves as a document embedding  Finally, we use two fully connected layers with ReLU (30-dimensional) and softmax (the same dimensionality as the number of classes) activations to obtain the final predictions 
With this approach, we overcome BERT's computational complexity, reducing it to $O(n/k * k^2) = O(nk)$ for RoBERT, with $k$ denoting the segment size (the LSTM component has negligible linear complexity $O(k)$)  The positional embeddings are also no longer an issue 
Method ::: Transformer over BERT
Given that Transformers' edge over recurrent networks is their ability to effectively capture long distance relationships between words in a sequence BIBREF0, we experiment with replacing the LSTM recurrent layer in favor of a small Transformer model (2 layers of transformer building block containing self-attention, fully connected, etc )  To investigate if preserving the information about the input sequence order is important, we also build a variant of ToBERT which learns positional embeddings at the segment-level representations (but is limited to sequences of length seen during the training) 
ToBERT's computational complexity $O(\frac{n^2}{k^2})$ is asymptotically inferior to RoBERT, as the top-level Transformer model again suffers from quadratic complexity in the number of segments  However, in practice this number is much smaller than the input sequence length (${\frac{n}{k}} << n$), so we haven't observed performance or memory issues with our datasets 
Experiments
We evaluated our models on 3 different datasets:
CSAT dataset for CSAT prediction, consisting of spoken transcripts (automatic via ASR) 
20 newsgroups for topic identification task, consisting of written text;
Fisher Phase 1 corpus for topic identification task, consisting of spoken transcripts (manual);
Experiments ::: CSAT
CSAT dataset consists of US English telephone speech from call centers  For each call in this dataset, customers participated in that call gave a rating on his experience with agent  Originally, this dataset has labels rated on a scale 1-9 with 9 being extremely satisfied and 1 being extremely dissatisfied  Fig  FIGREF16 shows the histogram of ratings for our dataset  As the distribution is skewed towards extremes, we choose to do binary classification with ratings above 4 5 as satisfied and below 4 5 as dissatisfied  Quantization of ratings also helped us to create a balanced dataset  This dataset contains 4331 calls and we split them into 3 sets for our experiments: 2866 calls for training, 362 calls for validation and, finally, 1103 calls for testing 
We obtained the transcripts by employing an ASR system  The ASR system uses TDNN-LSTM acoustic model trained on Fisher and Switchboard datasets with lattice-free maximum mutual information criterion BIBREF18  The word error rates using four-gram language models were 9 2% and 17 3% respectively on Switchboard and CallHome portions of Eval2000 dataset 
Experiments ::: 20 newsgroups
20 newsgroups data set is one of the frequently used datasets in the text processing community for text classification and text clustering  This data set contains approximately 20,000 English documents from 20 topics to be identified, with 11314 documents for training and 7532 for testing  In this work, we used only 90% of documents for training and the remaining 10% for validation  For fair comparison with other publications, we used 53160 words vocabulary set available in the datasets website 
Experiments ::: Fisher
Fisher Phase 1 US English corpus is often used for automatic speech recognition in speech community  In this work, we used it for topic identification as in BIBREF3  The documents are 10-minute long telephone conversations between two people discussing a given topic  We used same training and test splits as BIBREF3 in which 1374 and 1372 documents are used for training and testing respectively  For validation of our model, we used 10% of training dataset and the remaining 90% was used for actual model training  The number of topics in this data set is 40 
Experiments ::: Dataset Statistics
Table TABREF22 shows statistics of our datasets  It can be observed that average length of Fisher is much higher than 20 newsgroups and CSAT  Cumulative distribution of document lengths for each dataset is shown in Fig  FIGREF21  It can be observed that almost all of the documents in Fisher dataset have length more than 1000 words  For CSAT, more than 50% of the documents have length greater than 500 and for 20newsgroups only 10% of the documents have length greater than 500  Note that, for CSAT and 20newsgroups, there are few documents with length more than 5000 
Experiments ::: Architecture and Training Details
In this work, we split document into segments of 200 tokens with a shift of 50 tokens to extract features from BERT model  For RoBERT, LSTM model is trained to minimize cross-entropy loss with Adam optimizer BIBREF19  The initial learning rate is set to $0 001$ and is reduced by a factor of $0 95$ if validation loss does not decrease for 3-epochs  For ToBERT, the Transformer is trained with the default BERT version of Adam optimizer BIBREF1 with an initial learning rate of $5e$-5  We report accuracy in all of our experiments  We chose a model with the best validation accuracy to calculate accuracy on the test set  To accomodate for non-determinism of some TensorFlow GPU operations, we report accuracy averaged over 5 runs 
Results
Table TABREF25 presents results using pre-trained BERT features  We extracted features from the pooled output of final transformer block as these were shown to be working well for most of the tasks BIBREF1  The features extracted from a pre-trained BERT model without any fine-tuning lead to a sub-par performance  However, We also notice that ToBERT model exploited the pre-trained BERT features better than RoBERT  It also converged faster than RoBERT  Table TABREF26 shows results using features extracted after fine-tuning BERT model with our datasets  Significant improvements can be observed compared to using pre-trained BERT features  Also, it can be noticed that ToBERT outperforms RoBERT on Fisher and 20newsgroups dataset by 13 63% and 0 81% respectively  On CSAT, ToBERT performs slightly worse than RoBERT but it is not statistically significant as this dataset is small 
Table TABREF27 presents results using fine-tuned BERT predictions instead of the pooled output from final transformer block  For each document, having obtained segment-wise predictions we can obtain final prediction for the whole document in three ways:
Compute the average of all segment-wise predictions and find the most probable class;
Find the most frequently predicted class;
Train a classification model 
It can be observed from Table TABREF27 that a simple averaging operation or taking most frequent predicted class works competitively for CSAT and 20newsgroups but not for the Fisher dataset  We believe the improvements from using RoBERT or ToBERT, compared to simple averaging or most frequent operations, are proportional to the fraction of long documents in the dataset  CSAT and 20newsgroups have (on average) significantly shorter documents than Fisher, as seen in Fig  FIGREF21  Also, significant improvements for Fisher could be because of less confident predictions from BERT model as this dataset has 40 classes  Fig  FIGREF31 presents the comparison of average voting and ToBERT for various document length ranges for Fisher dataset  We used fine-tuned BERT segment-level predictions (P) for this analysis  It can be observed that ToBERT outperforms average voting in every interval  To the best of our knowledge, this is a state-of-the-art result reported on the Fisher dataset 
Table TABREF32 presents the effect of position embeddings on the model performance  It can be observed that position embeddings did not significantly affect the model performance for Fisher and 20newsgroups, but they helped slightly in CSAT prediction (an absolute improvement of 0 64% F1-score)  We think that this is explained by the fact that Fisher and 20newsgroups are topic identification tasks, and the topic does not change much throughout these documents  However, CSAT may vary during the call, and in some cases a naive assumption that the sequential nature of the transcripts is irrelevant may lead to wrong conclusions 
Table TABREF33 compares our results with previous works  It can be seen that our model ToBERT outperforms CNN based experiments by significant margin on CSAT and Fisher datasets  For CSAT dataset, we used multi-scale CNN (MS-CNN) as the baseline, given its strong results on Fisher and 20newsgroups  The setup was replicated from BIBREF5 for comparison  We also see that our result on 20 newsgroups is 0 6% worse than the state-of-the-art 
Conclusions
In this paper, we presented two methods for long documents using BERT model: RoBERT and ToBERT  We evaluated our experiments on two classification tasks - customer satisfaction prediction and topic identification - using 3 datasets: CSAT, 20newsgroups and Fisher  We observed that ToBERT outperforms RoBERT on pre-trained BERT features and fine-tuned BERT features for all our tasks  Also, we noticed that fine-tuned BERT performs better than pre-trained BERT  We have shown that both RoBERT and ToBERT improved the simple baselines of taking an average (or the most frequent) of segment-wise predictions for long documents to obtain final prediction  Position embeddings did not significantly affect our models performance, but slightly improved the accuracy on the CSAT task  We obtained the best results on Fisher dataset and good improvements for CSAT task compared to the CNN baseline  It is interesting to note that the longer the average input in a given task, the bigger improvement we observe w r t  the baseline for that task  Our results confirm that both RoBERT and ToBERT can be used for long sequences with competitive performance and quick fine-tuning procedure  For future work, we shall focus on training models on long documents directly (i e  in an end-to-end manner) 
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: BIBREF17, BIBREF18, TensiStrength BIBREF13, TwitterNLP BIBREF6, BIBREF19, CogComp-NLP BIBREF20, Stanford NLP NER BIBREF21

BIBREF23, BIBREF17, BIBREF18, BIBREF19, BIBREF24, BIBREF25, BIBREF26

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. On top of BERT does the RNN layer work better or the transformer layer?
Context 4: Introduction
The Transformer architecture BIBREF0 for deep neural networks has quickly risen to prominence in NLP through its efficiency and performance, leading to improvements in the state of the art of Neural Machine Translation BIBREF1, BIBREF2, as well as inspiring other powerful general-purpose models like BERT BIBREF3 and GPT-2 BIBREF4  At the heart of the Transformer lie multi-head attention mechanisms: each word is represented by multiple different weighted averages of its relevant context  As suggested by recent works on interpreting attention head roles, separate attention heads may learn to look for various relationships between tokens BIBREF5, BIBREF6, BIBREF7, BIBREF8, BIBREF9 
The attention distribution of each head is predicted typically using the softmax normalizing transform  As a result, all context words have non-zero attention weight  Recent work on single attention architectures suggest that using sparse normalizing transforms in attention mechanisms such as sparsemax – which can yield exactly zero probabilities for irrelevant words – may improve performance and interpretability BIBREF12, BIBREF13, BIBREF14  Qualitative analysis of attention heads BIBREF0 suggests that, depending on what phenomena they capture, heads tend to favor flatter or more peaked distributions 
Recent works have proposed sparse Transformers BIBREF10 and adaptive span Transformers BIBREF11  However, the “sparsity" of those models only limits the attention to a contiguous span of past tokens, while in this work we propose a highly adaptive Transformer model that is capable of attending to a sparse set of words that are not necessarily contiguous  Figure FIGREF1 shows the relationship of these methods with ours 
Our contributions are the following:
We introduce sparse attention into the Transformer architecture, showing that it eases interpretability and leads to slight accuracy gains 
We propose an adaptive version of sparse attention, where the shape of each attention head is learnable and can vary continuously and dynamically between the dense limit case of softmax and the sparse, piecewise-linear sparsemax case 
We make an extensive analysis of the added interpretability of these models, identifying both crisper examples of attention head behavior observed in previous work, as well as novel behaviors unraveled thanks to the sparsity and adaptivity of our proposed model 
Background ::: The Transformer
In NMT, the Transformer BIBREF0 is a sequence-to-sequence (seq2seq) model which maps an input sequence to an output sequence through hierarchical multi-head attention mechanisms, yielding a dynamic, context-dependent strategy for propagating information within and across sentences  It contrasts with previous seq2seq models, which usually rely either on costly gated recurrent operations BIBREF15, BIBREF16 or static convolutions BIBREF17 
Given $n$ query contexts and $m$ sequence items under consideration, attention mechanisms compute, for each query, a weighted representation of the items  The particular attention mechanism used in BIBREF0 is called scaled dot-product attention, and it is computed in the following way:
where $\mathbf {Q} \in \mathbb {R}^{n \times d}$ contains representations of the queries, $\mathbf {K}, \mathbf {V} \in \mathbb {R}^{m \times d}$ are the keys and values of the items attended over, and $d$ is the dimensionality of these representations  The $\mathbf {\pi }$ mapping normalizes row-wise using softmax, $\mathbf {\pi }(\mathbf {Z})_{ij} = \operatornamewithlimits{\mathsf {softmax}}(\mathbf {z}_i)_j$, where
In words, the keys are used to compute a relevance score between each item and query  Then, normalized attention weights are computed using softmax, and these are used to weight the values of each item at each query context 
However, for complex tasks, different parts of a sequence may be relevant in different ways, motivating multi-head attention in Transformers  This is simply the application of Equation DISPLAY_FORM7 in parallel $H$ times, each with a different, learned linear transformation that allows specialization:
In the Transformer, there are three separate multi-head attention mechanisms for distinct purposes:
Encoder self-attention: builds rich, layered representations of each input word, by attending on the entire input sentence 
Context attention: selects a representative weighted average of the encodings of the input words, at each time step of the decoder 
Decoder self-attention: attends over the partial output sentence fragment produced so far 
Together, these mechanisms enable the contextualized flow of information between the input sentence and the sequential decoder 
Background ::: Sparse Attention
The softmax mapping (Equation DISPLAY_FORM8) is elementwise proportional to $\exp $, therefore it can never assign a weight of exactly zero  Thus, unnecessary items are still taken into consideration to some extent  Since its output sums to one, this invariably means less weight is assigned to the relevant items, potentially harming performance and interpretability BIBREF18  This has motivated a line of research on learning networks with sparse mappings BIBREF19, BIBREF20, BIBREF21, BIBREF22  We focus on a recently-introduced flexible family of transformations, $\alpha $-entmax BIBREF23, BIBREF14, defined as:
where $\triangle ^d \lbrace \mathbf {p}\in \mathbb {R}^d:\sum _{i} p_i = 1\rbrace $ is the probability simplex, and, for $\alpha \ge 1$, $\mathsf {H}^{\textsc {T}}_\alpha $ is the Tsallis continuous family of entropies BIBREF24:
This family contains the well-known Shannon and Gini entropies, corresponding to the cases $\alpha =1$ and $\alpha =2$, respectively 
Equation DISPLAY_FORM14 involves a convex optimization subproblem  Using the definition of $\mathsf {H}^{\textsc {T}}_\alpha $, the optimality conditions may be used to derive the following form for the solution (Appendix SECREF83):
where $[\cdot ]_+$ is the positive part (ReLU) function, $\mathbf {1}$ denotes the vector of all ones, and $\tau $ – which acts like a threshold – is the Lagrange multiplier corresponding to the $\sum _i p_i=1$ constraint 
Background ::: Sparse Attention ::: Properties of @!START@$\alpha $@!END@-entmax 
The appeal of $\alpha $-entmax for attention rests on the following properties  For $\alpha =1$ (i e , when $\mathsf {H}^{\textsc {T}}_\alpha $ becomes the Shannon entropy), it exactly recovers the softmax mapping (We provide a short derivation in Appendix SECREF89 )  For all $\alpha >1$ it permits sparse solutions, in stark contrast to softmax  In particular, for $\alpha =2$, it recovers the sparsemax mapping BIBREF19, which is piecewise linear  In-between, as $\alpha $ increases, the mapping continuously gets sparser as its curvature changes 
To compute the value of $\alpha $-entmax, one must find the threshold $\tau $ such that the r h s  in Equation DISPLAY_FORM16 sums to one  BIBREF23 propose a general bisection algorithm  BIBREF14 introduce a faster, exact algorithm for $\alpha =1 5$, and enable using $\mathop {\mathsf {\alpha }\textnormal {-}\mathsf {entmax }}$ with fixed $\alpha $ within a neural network by showing that the $\alpha $-entmax Jacobian w r t  $\mathbf {z}$ for $\mathbf {p}^\star = \mathop {\mathsf {\alpha }\textnormal {-}\mathsf {entmax }}(\mathbf {z})$ is
Our work furthers the study of $\alpha $-entmax by providing a derivation of the Jacobian w r t  the hyper-parameter $\alpha $ (Section SECREF3), thereby allowing the shape and sparsity of the mapping to be learned automatically  This is particularly appealing in the context of multi-head attention mechanisms, where we shall show in Section SECREF35 that different heads tend to learn different sparsity behaviors 
Adaptively Sparse Transformers with @!START@$\alpha $@!END@-entmax
We now propose a novel Transformer architecture wherein we simply replace softmax with $\alpha $-entmax in the attention heads  Concretely, we replace the row normalization $\mathbf {\pi }$ in Equation DISPLAY_FORM7 by
This change leads to sparse attention weights, as long as $\alpha >1$; in particular, $\alpha =1 5$ is a sensible starting point BIBREF14 
Adaptively Sparse Transformers with @!START@$\alpha $@!END@-entmax ::: Different @!START@$\alpha $@!END@ per head 
Unlike LSTM-based seq2seq models, where $\alpha $ can be more easily tuned by grid search, in a Transformer, there are many attention heads in multiple layers  Crucial to the power of such models, the different heads capture different linguistic phenomena, some of them isolating important words, others spreading out attention across phrases BIBREF0  This motivates using different, adaptive $\alpha $ values for each attention head, such that some heads may learn to be sparser, and others may become closer to softmax  We propose doing so by treating the $\alpha $ values as neural network parameters, optimized via stochastic gradients along with the other weights 
Adaptively Sparse Transformers with @!START@$\alpha $@!END@-entmax ::: Derivatives w r t  @!START@$\alpha $@!END@ 
In order to optimize $\alpha $ automatically via gradient methods, we must compute the Jacobian of the entmax output w r t  $\alpha $  Since entmax is defined through an optimization problem, this is non-trivial and cannot be simply handled through automatic differentiation; it falls within the domain of argmin differentiation, an active research topic in optimization BIBREF25, BIBREF26 
One of our key contributions is the derivation of a closed-form expression for this Jacobian  The next proposition provides such an expression, enabling entmax layers with adaptive $\alpha $  To the best of our knowledge, ours is the first neural network module that can automatically, continuously vary in shape away from softmax and toward sparse mappings like sparsemax 
Proposition 1 Let $\mathbf {p}^\star \mathop {\mathsf {\alpha }\textnormal {-}\mathsf {entmax }}(\mathbf {z})$ be the solution of Equation DISPLAY_FORM14  Denote the distribution $\tilde{p}_i {(p_i^\star )^{2 - \alpha }}{ \sum _j(p_j^\star )^{2-\alpha }}$ and let $h_i -p^\star _i \log p^\star _i$  The $i$th component of the Jacobian $\mathbf {g} \frac{\partial \mathop {\mathsf {\alpha }\textnormal {-}\mathsf {entmax }}(\mathbf {z})}{\partial \alpha }$ is
proof uses implicit function differentiation and is given in Appendix SECREF10 
Proposition UNKREF22 provides the remaining missing piece needed for training adaptively sparse Transformers  In the following section, we evaluate this strategy on neural machine translation, and analyze the behavior of the learned attention heads 
Experiments
We apply our adaptively sparse Transformers on four machine translation tasks  For comparison, a natural baseline is the standard Transformer architecture using the softmax transform in its multi-head attention mechanisms  We consider two other model variants in our experiments that make use of different normalizing transformations:
1 5-entmax: a Transformer with sparse entmax attention with fixed $\alpha =1 5$ for all heads  This is a novel model, since 1 5-entmax had only been proposed for RNN-based NMT models BIBREF14, but never in Transformers, where attention modules are not just one single component of the seq2seq model but rather an integral part of all of the model components 
$\alpha $-entmax: an adaptive Transformer with sparse entmax attention with a different, learned $\alpha _{i,j}^t$ for each head 
The adaptive model has an additional scalar parameter per attention head per layer for each of the three attention mechanisms (encoder self-attention, context attention, and decoder self-attention), i e ,
and we set $\alpha _{i,j}^t = 1 + \operatornamewithlimits{\mathsf {sigmoid}}(a_{i,j}^t) \in ]1, 2[$  All or some of the $\alpha $ values can be tied if desired, but we keep them independent for analysis purposes 
Experiments ::: Datasets 
Our models were trained on 4 machine translation datasets of different training sizes:
[itemsep= 5ex,leftmargin=2ex]
IWSLT 2017 German $\rightarrow $ English BIBREF27: 200K sentence pairs 
KFTT Japanese $\rightarrow $ English BIBREF28: 300K sentence pairs 
WMT 2016 Romanian $\rightarrow $ English BIBREF29: 600K sentence pairs 
WMT 2014 English $\rightarrow $ German BIBREF30: 4 5M sentence pairs 
All of these datasets were preprocessed with byte-pair encoding BIBREF31, using joint segmentations of 32k merge operations 
Experiments ::: Training 
We follow the dimensions of the Transformer-Base model of BIBREF0: The number of layers is $L=6$ and number of heads is $H=8$ in the encoder self-attention, the context attention, and the decoder self-attention  We use a mini-batch size of 8192 tokens and warm up the learning rate linearly until 20k steps, after which it decays according to an inverse square root schedule  All models were trained until convergence of validation accuracy, and evaluation was done at each 10k steps for ro$\rightarrow $en and en$\rightarrow $de and at each 5k steps for de$\rightarrow $en and ja$\rightarrow $en  The end-to-end computational overhead of our methods, when compared to standard softmax, is relatively small; in training tokens per second, the models using $\alpha $-entmax and $1 5$-entmax are, respectively, $75\%$ and $90\%$ the speed of the softmax model 
Experiments ::: Results 
We report test set tokenized BLEU BIBREF32 results in Table TABREF27  We can see that replacing softmax by entmax does not hurt performance in any of the datasets; indeed, sparse attention Transformers tend to have slightly higher BLEU, but their sparsity leads to a better potential for analysis  In the next section, we make use of this potential by exploring the learned internal mechanics of the self-attention heads 
Analysis
We conduct an analysis for the higher-resource dataset WMT 2014 English $\rightarrow $ German of the attention in the sparse adaptive Transformer model ($\alpha $-entmax) at multiple levels: we analyze high-level statistics as well as individual head behavior  Moreover, we make a qualitative analysis of the interpretability capabilities of our models 
Analysis ::: High-Level Statistics ::: What kind of @!START@$\alpha $@!END@ values are learned?
Figure FIGREF37 shows the learning trajectories of the $\alpha $ parameters of a selected subset of heads  We generally observe a tendency for the randomly-initialized $\alpha $ parameters to decrease initially, suggesting that softmax-like behavior may be preferable while the model is still very uncertain  After around one thousand steps, some heads change direction and become sparser, perhaps as they become more confident and specialized  This shows that the initialization of $\alpha $ does not predetermine its sparsity level or the role the head will have throughout  In particular, head 8 in the encoder self-attention layer 2 first drops to around $\alpha =1 3$ before becoming one of the sparsest heads, with $\alpha \approx 2$ 
The overall distribution of $\alpha $ values at convergence can be seen in Figure FIGREF38  We can observe that the encoder self-attention blocks learn to concentrate the $\alpha $ values in two modes: a very sparse one around $\alpha \rightarrow 2$, and a dense one between softmax and 1 5-entmax   However, the decoder self and context attention only learn to distribute these parameters in a single mode  We show next that this is reflected in the average density of attention weight vectors as well 
Analysis ::: High-Level Statistics ::: Attention weight density when translating 
For any $\alpha >1$, it would still be possible for the weight matrices in Equation DISPLAY_FORM9 to learn re-scalings so as to make attention sparser or denser  To visualize the impact of adaptive $\alpha $ values, we compare the empirical attention weight density (the average number of tokens receiving non-zero attention) within each module, against sparse Transformers with fixed $\alpha =1 5$ 
Figure FIGREF40 shows that, with fixed $\alpha =1 5$, heads tend to be sparse and similarly-distributed in all three attention modules  With learned $\alpha $, there are two notable changes: (i) a prominent mode corresponding to fully dense probabilities, showing that our models learn to combine sparse and dense attention, and (ii) a distinction between the encoder self-attention – whose background distribution tends toward extreme sparsity – and the other two modules, who exhibit more uniform background distributions  This suggests that perhaps entirely sparse Transformers are suboptimal 
The fact that the decoder seems to prefer denser attention distributions might be attributed to it being auto-regressive, only having access to past tokens and not the full sentence  We speculate that it might lose too much information if it assigned weights of zero to too many tokens in the self-attention, since there are fewer tokens to attend to in the first place 
Teasing this down into separate layers, Figure FIGREF41 shows the average (sorted) density of each head for each layer  We observe that $\alpha $-entmax is able to learn different sparsity patterns at each layer, leading to more variance in individual head behavior, to clearly-identified dense and sparse heads, and overall to different tendencies compared to the fixed case of $\alpha =1 5$ 
Analysis ::: High-Level Statistics ::: Head diversity 
To measure the overall disagreement between attention heads, as a measure of head diversity, we use the following generalization of the Jensen-Shannon divergence:
where $\mathbf {p}_j$ is the vector of attention weights assigned by head $j$ to each word in the sequence, and $\mathsf {H}^\textsc {S}$ is the Shannon entropy, base-adjusted based on the dimension of $\mathbf {p}$ such that $JS \le 1$  We average this measure over the entire validation set  The higher this metric is, the more the heads are taking different roles in the model 
Figure FIGREF44 shows that both sparse Transformer variants show more diversity than the traditional softmax one

ground_truth: Transformer over BERT (ToBERT)

The transformer layer

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:
[noitemsep]
- 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