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 method's improvements of F1 for NER task for English and Chinese datasets?
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 
Context 2: 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: English datasets including CoNLL2003 and OntoNotes5.0, our proposed method outperforms BERT-MRCBIBREF38 by +0.29 and +0.96 respectively, Chinese datasets, achieving F1 improvements by +0.97 and +2.36 on MSRA and OntoNotes4.0, respectively

For English datasets including CoNLL2003 and OntoNotes5.0, our proposed method outperforms BERT-MRCBIBREF38 by +0.29 and +0.96 respectively., huge performance boosts on Chinese datasets, achieving F1 improvements by +0.97 and +2.36 on MSRA and OntoNotes4.0, respectively

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 2:  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) 
Context 3: Introduction
Pretrained Language Models (PTLMs) such as BERT BIBREF1 have spearheaded advances on many NLP tasks  Usually, PTLMs are pretrained on unlabeled general-domain and/or mixed-domain text, such as Wikipedia, digital books or the Common Crawl corpus 
When applying PTLMs to specific domains, it can be useful to domain-adapt them  Domain adaptation of PTLMs has typically been achieved by pretraining on target-domain text  One such model is BioBERT BIBREF2, which was initialized from general-domain BERT and then pretrained on biomedical scientific publications  The domain adaptation is shown to be helpful for target-domain tasks such as biomedical Named Entity Recognition (NER) or Question Answering (QA)  On the downside, the computational cost of pretraining can be considerable: BioBERTv1 0 was adapted for ten days on eight large GPUs (see Table TABREF1), which is expensive, environmentally unfriendly, prohibitive for small research labs and students, and may delay prototyping on emerging domains 
We therefore propose a fast, CPU-only domain-adaptation method for PTLMs: We train Word2Vec BIBREF3 on target-domain text and align the resulting word vectors with the wordpiece vectors of an existing general-domain PTLM  The PTLM thus gains domain-specific lexical knowledge in the form of additional word vectors, but its deeper layers remain unchanged  Since Word2Vec and the vector space alignment are efficient models, the process requires a fraction of the resources associated with pretraining the PTLM itself, and it can be done on CPU 
In Section SECREF4, we use the proposed method to domain-adapt BERT on PubMed+PMC (the data used for BioBERTv1 0) and/or CORD-19 (Covid-19 Open Research Dataset)  We improve over general-domain BERT on eight out of eight biomedical NER tasks, using a fraction of the compute cost associated with BioBERT  In Section SECREF5, we show how to quickly adapt an existing Question Answering model to text about the Covid-19 pandemic, without any target-domain Language Model pretraining or finetuning 
Related work ::: The BERT PTLM
For our purpose, a PTLM consists of three parts: A tokenizer $\mathcal {T}_\mathrm {LM} : \mathbb {L}^+ \rightarrow \mathbb {L}_\mathrm {LM}^+$, a wordpiece embedding function $\mathcal {E}_\mathrm {LM}: \mathbb {L}_\mathrm {LM} \rightarrow \mathbb {R}^{d_\mathrm {LM}}$ and an encoder function $\mathcal {F}_\mathrm {LM}$  $\mathbb {L}_\mathrm {LM}$ is a limited vocabulary of wordpieces  All words that are not in $\mathbb {L}_\mathrm {LM}$ are tokenized into sequences of shorter wordpieces, e g , tachycardia becomes ta ##chy ##card ##ia  Given a sentence $S = [w_1, \ldots , w_T]$, tokenized as $\mathcal {T}_\mathrm {LM}(S) = [\mathcal {T}_\mathrm {LM}(w_1); \ldots ; \mathcal {T}_\mathrm {LM}(w_T)]$, $\mathcal {E}_\mathrm {LM}$ embeds every wordpiece in $\mathcal {T}_\mathrm {LM}(S)$ into a real-valued, trainable wordpiece vector  The wordpiece vectors of the entire sequence are stacked and fed into $\mathcal {F}_\mathrm {LM}$  Note that we consider position and segment embeddings to be a part of $\mathcal {F}_\mathrm {LM}$ rather than $\mathcal {E}_\mathrm {LM}$ 
In the case of BERT, $\mathcal {F}_\mathrm {LM}$ is a Transformer BIBREF4, followed by a final Feed-Forward Net  During pretraining, the Feed-Forward Net predicts the identity of masked wordpieces  When finetuning on a supervised task, it is usually replaced with a randomly initialized task-specific layer 
Related work ::: Domain-adapted PTLMs
Domain adaptation of PTLMs is typically achieved by pretraining on unlabeled target-domain text  Some examples of such models are BioBERT BIBREF2, which was pretrained on the PubMed and/or PubMed Central (PMC) corpora, SciBERT BIBREF5, which was pretrained on papers from SemanticScholar, ClinicalBERT BIBREF6, BIBREF7 and ClinicalXLNet BIBREF8, which were pretrained on clinical patient notes, and AdaptaBERT BIBREF9, which was pretrained on Early Modern English text  In most cases, a domain-adapted PTLM is initialized from a general-domain PTLM (e g , standard BERT), though BIBREF5 report better results with a model that was pretrained from scratch with a custom wordpiece vocabulary  In this paper, we focus on BioBERT, as its domain adaptation corpora are publicly available 
Related work ::: Word vectors
Word vectors are distributed representations of words that are trained on unlabeled text  Contrary to PTLMs, word vectors are non-contextual, i e , a word type is always assigned the same vector, regardless of context  In this paper, we use Word2Vec BIBREF3 to train word vectors  We will denote the Word2Vec lookup function as $\mathcal {E}_\mathrm {W2V} : \mathbb {L}_\mathrm {W2V} \rightarrow \mathbb {R}^{d_\mathrm {W2V}}$ 
Related work ::: Word vector space alignment
Word vector space alignment has most frequently been explored in the context of cross-lingual word embeddings  For instance, BIBREF10 align English and Spanish Word2Vec spaces by a simple linear transformation  BIBREF11 use a related method to align cross-lingual word vectors and multilingual BERT wordpiece vectors 
Method
In the following, we assume access to a general-domain PTLM, as described in Section SECREF2, and a corpus of unlabeled target-domain text 
Method ::: Creating new input vectors
In a first step, we train Word2Vec on the target-domain corpus  In a second step, we take the intersection of $\mathbb {L}_\mathrm {LM}$ and $\mathbb {L}_\mathrm {W2V}$  In practice, the intersection mostly contains wordpieces from $\mathbb {L}_\mathrm {LM}$ that correspond to standalone words  It also contains single characters and other noise, however, we found that filtering them does not improve alignment quality  In a third step, we use the intersection to fit an unconstrained linear transformation $\mathbf {W} \in \mathbb {R}^{d_\mathrm {LM} \times d_\mathrm {W2V}}$ via least squares:
Intuitively, $\mathbf {W}$ makes Word2Vec vectors “look like” the PTLM's native wordpiece vectors, just like cross-lingual alignment makes word vectors from one language “look like” word vectors from another language  In Table TABREF7 (top), we show examples of within-space and cross-space nearest neighbors after alignment 
Method ::: Updating the wordpiece embedding layer
Next, we redefine the wordpiece embedding layer of the PTLM  The most radical strategy would be to replace the entire layer with the aligned Word2Vec vectors:
In initial experiments, this strategy led to a drop in performance, presumably because function words are not well represented by Word2Vec, and replacing them disrupts BERT's syntactic abilities  To prevent this problem, we leave existing wordpiece vectors intact and only add new ones:
Method ::: Updating the tokenizer
In a final step, we update the tokenizer to account for the added words  Let $\mathcal {T}_\mathrm {LM}$ be the standard BERT tokenizer, and let $\hat{\mathcal {T}}_\mathrm {LM}$ be the tokenizer that treats all words in $\mathbb {L}_\mathrm {LM} \cup \mathbb {L}_\mathrm {W2V}$ as one-wordpiece tokens, while tokenizing any other words as usual 
In practice, a given word may or may not benefit from being tokenized by $\hat{\mathcal {T}}_\mathrm {LM}$ instead of $\mathcal {T}_\mathrm {LM}$  To give a concrete example, 82% of the words in the BC5CDR NER dataset that end in the suffix -ia are inside a disease entity (e g , tachycardia)  $\mathcal {T}_\mathrm {LM}$ tokenizes this word as ta ##chy ##card ##ia, thereby exposing the orthographic cue to the model  As a result, $\mathcal {T}_\mathrm {LM}$ leads to higher recall on -ia diseases  But there are many cases where wordpiece tokenization is meaningless or misleading  For instance euthymia (not a disease) is tokenized by $\mathcal {T}_\mathrm {LM}$ as e ##uth ##ym ##ia, making it likely to be classified as a disease  By contrast, $\hat{\mathcal {T}}_\mathrm {LM}$ gives euthymia a one-wordpiece representation that depends only on distributional semantics  We find that using $\hat{\mathcal {T}}_\mathrm {LM}$ improves precision on -ia diseases 
To combine these complementary strengths, we use a 50/50 mixture of $\mathcal {T}_\mathrm {LM}$-tokenization and $\hat{\mathcal {T}}_\mathrm {LM}$-tokenization when finetuning the PTLM on a task  At test time, we use both tokenizers and mean-pool the outputs  Let $o(\mathcal {T}(S))$ be some output of interest (e g , a logit), given sentence $S$ tokenized by $\mathcal {T}$  We predict:
Experiment 1: Biomedical NER
In this section, we use the proposed method to create GreenBioBERT, an inexpensive and environmentally friendly alternative to BioBERT  Recall that BioBERTv1 0 (biobert_v1 0_pubmed_pmc) was initialized from general-domain BERT (bert-base-cased) and pretrained on PubMed+PMC 
Experiment 1: Biomedical NER ::: Domain adaptation
We train Word2Vec with vector size $d_\mathrm {W2V} = d_\mathrm {LM} = 768$ on PubMed+PMC (see Appendix for details)  Then, we follow the procedure described in Section SECREF3 to update the wordpiece embedding layer and tokenizer of general-domain BERT 
Experiment 1: Biomedical NER ::: Finetuning
We finetune GreenBioBERT on the eight publicly available NER tasks used in BIBREF2  We also do reproduction experiments with general-domain BERT and BioBERTv1 0, using the same setup as our model  We average results over eight random seeds  See Appendix for details on preprocessing, training and hyperparameters 
Experiment 1: Biomedical NER ::: Results and discussion
Table TABREF7 (bottom) shows entity-level precision, recall and F1  For ease of visualization, Figure FIGREF13 shows what portion of the BioBERT – BERT F1 delta is covered  We improve over general-domain BERT on all tasks with varying effect sizes

ground_truth: MEDDOCAN, NUBes-PHI

MEDDOCAN, NUBes 

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 eight NER tasks did they evaluate on?
Context 3:  Depending on the points of reference, we cover an average 52% to 60% of the BioBERT – BERT F1 delta (54% for BioBERTv1 0, 60% for BioBERTv1 1 and 52% for our reproduction experiments)  Table TABREF17 (top) shows the importance of vector space alignment: If we replace the aligned Word2Vec vectors with their non-aligned counterparts (by setting $\mathbf {W} = \mathbf {1}$) or with randomly initialized vectors, F1 drops on all tasks 
Experiment 2: Covid-19 QA
In this section, we use the proposed method to quickly adapt an existing general-domain QA model to an emerging target domain: Covid-19  Our baseline model is SQuADBERT (bert-large-uncased-whole-word-masking-finetuned-squad), a version of BERT that was finetuned on general-domain SQuAD BIBREF19  We evaluate on Deepset-AI Covid-QA, a SQuAD-style dataset with 1380 questions (see Appendix for details on data and preprocessing)  We assume that there is no target-domain finetuning data, which is a realistic setup for a new domain 
Experiment 2: Covid-19 QA ::: Domain adaptation
We train Word2Vec with vector size $d_\mathrm {W2V} = d_\mathrm {LM} = 1024$ on CORD-19 (Covid-19 Open Research Dataset) and/or PubMed+PMC  The process takes less than an hour on CORD-19 and about one day on the combined corpus, again without the need for a GPU  Then, we update SQuADBERT's wordpiece embedding layer and tokenizer, as described in Section SECREF3  We refer to the resulting model as GreenCovidSQuADBERT 
Experiment 2: Covid-19 QA ::: Results and discussion
Table TABREF17 (bottom) shows that GreenCovidSQuADBERT outperforms general-domain SQuADBERT in all metrics  Most of the improvement can be achieved with just the small CORD-19 corpus, which is more specific to the target domain (compare “Cord-19 only” and “Cord-19+PubMed+PMC”) 
Conclusion
As a reaction to the trend towards high-resource models, we have proposed an inexpensive, CPU-only method for domain-adapting Pretrained Language Models: We train Word2Vec vectors on target-domain data and align them with the wordpiece vector space of a general-domain PTLM 
On eight biomedical NER tasks, we cover over 50% of the BioBERT – BERT F1 delta, at 5% of BioBERT's domain adaptation CO$_2$ footprint and 2% of its cloud compute cost  We have also shown how to rapidly adapt an existing BERT QA model to an emerging domain – the Covid-19 pandemic – without the need for target-domain Language Model pretraining or finetuning 
We hope that our approach will benefit practitioners with limited time or resources, and that it will encourage environmentally friendlier NLP 
Inexpensive Domain Adaptation of Pretrained Language Models (Appendix) ::: Word2Vec training
We downloaded the PubMed, PMC and CORD-19 corpora from:
https://ftp ncbi nlm nih gov/pub/pmc/oa_bulk/ [20 January 2020, 68GB raw text]
https://ftp ncbi nlm nih gov/pubmed/baseline/ [20 January 2020, 24GB raw text]
https://pages semanticscholar org/coronavirus-research [17 April 2020, 2GB raw text]
We extract all abstracts and text bodies and apply the BERT basic tokenizer (a word tokenizer that standard BERT uses before wordpiece tokenization)  Then, we train CBOW Word2Vec with negative sampling  We use default parameters except for the vector size (which we set to $d_\mathrm {W2V} = d_\mathrm {LM}$) 
Inexpensive Domain Adaptation of Pretrained Language Models (Appendix) ::: Experiment 1: Biomedical NER ::: Pretrained models
General-domain BERT and BioBERTv1 0 were downloaded from:
https://storage googleapis com/bert_models/2018_10_18/cased_L-12_H-768_A-12 zip
https://github com/naver/biobert-pretrained
Inexpensive Domain Adaptation of Pretrained Language Models (Appendix) ::: Experiment 1: Biomedical NER ::: Data
We downloaded the NER datasets by following instructions on https://github com/dmis-lab/biobert#Datasets  For detailed dataset statistics, see BIBREF2 
Inexpensive Domain Adaptation of Pretrained Language Models (Appendix) ::: Experiment 1: Biomedical NER ::: Preprocessing
We cut all sentences into chunks of 30 or fewer whitespace-tokenized words (without splitting inside labeled spans)  Then, we tokenize every chunk $S$ with $\mathcal {T} = \mathcal {T}_\mathrm {LM}$ or $\mathcal {T} = \hat{\mathcal {T}}_\mathrm {LM}$ and add special tokens:
Word-initial wordpieces in $\mathcal {T}(S)$ are labeled as B(egin), I(nside) or O(utside), while non-word-initial wordpieces are labeled as X(ignore) 
Inexpensive Domain Adaptation of Pretrained Language Models (Appendix) ::: Experiment 1: Biomedical NER ::: Modeling, training and inference
We follow BIBREF2's implementation (https://github com/dmis-lab/biobert): We add a randomly initialized softmax classifier on top of the last BERT layer to predict the labels  We finetune the entire model to minimize negative log likelihood, with the standard Adam optimizer BIBREF20 and a linear learning rate scheduler (10% warmup)  Like BIBREF2, we finetune on the concatenation of the training and development set  All finetuning runs were done on a GeForce Titan X GPU (12GB) 
Since we do not have the resources for an extensive hyperparameter search, we use defaults and recommendations from the BioBERT repository: Batch size of 32, peak learning rate of $1 \cdot 10^{-5}$, and 100 epochs 
At inference time, we gather the output logits of word-initial wordpieces only  Since the number of word-initial wordpieces is the same for $\mathcal {T}_\mathrm {LM}(S)$ and $\hat{\mathcal {T}}_\mathrm {LM}(S)$, this makes mean-pooling the logits straightforward 
Inexpensive Domain Adaptation of Pretrained Language Models (Appendix) ::: Experiment 1: Biomedical NER ::: Note on our reproduction experiments
We found it easier to reproduce or exceed BIBREF2's results for general-domain BERT, compared to their results for BioBERTv1 0 (see Figure FIGREF13, main paper)  While this may be due to hyperparameters, it suggests that BioBERTv1 0 was more strongly tuned than BERT in the original BioBERT paper  This observation does not affect our conclusions, as GreenBioBERT performs better than reproduced BERT as well 
Inexpensive Domain Adaptation of Pretrained Language Models (Appendix) ::: Experiment 2: Covid-19 QA ::: Pretrained model
We downloaded the SQuADBERT baseline from:
https://huggingface co/bert-large-uncased-whole-word-masking-finetuned-squad
Inexpensive Domain Adaptation of Pretrained Language Models (Appendix) ::: Experiment 2: Covid-19 QA ::: Data
We downloaded the Deepset-AI Covid-QA dataset from:
https://github com/deepset-ai/COVID-QA/blob/master/data/question-answering/200423_covidQA json [24 April 2020]
At the time of writing, the dataset contains 1380 questions and gold answer spans  Every question is associated with one of 98 research papers (contexts)  We treat the entire dataset as a test set 
Note that there are some important differences between the dataset and SQuAD, which make the task challenging:
The contexts are full documents rather than single paragraphs  Thus, the correct answer may appear several times, often with slightly different wordings  Only a single one of the occurrences is annotated as correct, e g :
What was the prevalence of Coronavirus OC43 in community samples in Ilorin, Nigeria?
13 3% (95% CI 6 9-23 6%) # from main text
(13 3%, 10/75)  # from abstract
SQuAD gold answers are defined as the “shortest span in the paragraph that answered the question” BIBREF19, but many Covid-QA gold answers are longer and contain non-essential context, e g :
When was the Middle East Respiratory Syndrome Coronavirus isolated first?
(MERS-CoV) was first isolated in 2012, in a 60-year-old man who died in Jeddah, KSA due to severe acute pneumonia and multiple organ failure
2012,
Inexpensive Domain Adaptation of Pretrained Language Models (Appendix) ::: Experiment 2: Covid-19 QA ::: Preprocessing
We tokenize every question-context pair $(Q, C)$ with $\mathcal {T} = \mathcal {T}_\mathrm {LM}$ or $\mathcal {T} = \hat{\mathcal {T}}_\mathrm {LM}$, which yields $(\mathcal {T}(Q), \mathcal {T}(C))$  Since $\mathcal {T}(C)$ is usually too long to be digested in a single forward pass, we define a sliding window with width and stride $N = \mathrm {floor}(\frac{509 - |\mathcal {T}(Q)|}{2})$  At step $n$, the “active” window is between $a^{(l)}_n = nN$ and $a^{(r)}_n = \mathrm {min}(|C|, nN+N)$  The input is defined as:
$p^{(l)}_n$ and $p^{(r)}_n$ are chosen such that $|X^{(n)}| = 512$, and such that the active window is in the center of the input (if possible) 
Inexpensive Domain Adaptation of Pretrained Language Models (Appendix) ::: Experiment 2: Covid-19 QA ::: Modeling and inference
Feeding $X^{(n)}$ into the pretrained QA model yields start logits $\mathbf {h^{\prime }}^{(\mathrm {start}, n)} \in \mathbb {R}^{|X^{(n)}|}$ and end logits $\mathbf {h^{\prime }}^{(\mathrm {end},n)} \in \mathbb {R}^{|X^{(n)}|}$  We extract and concatenate the slices that correspond to the active windows of all steps:
Next, we map the logits from the wordpiece level to the word level  This allows us to mean-pool the outputs of $\mathcal {T}_\mathrm {LM}$ and $\hat{\mathcal {T}}_\mathrm {LM}$ even when $|\mathcal {T}_\mathrm {LM}(C)| \ne |\hat{\mathcal {T}}_\mathrm {LM}(C)|$ 
Let $c_i$ be a whitespace-delimited word in $C$  Let $\mathcal {T}(C)_{j:j+|\mathcal {T}(c_i)|}$ be the corresponding wordpieces  The start and end logits of $c_i$ are derived as:
Finally, we return the answer span $C_{k:k^{\prime }}$ that maximizes $o^{(\mathrm {start})}_k + o^{(\mathrm {end})}_{k^{\prime }}$, subject to the constraints that $k^{\prime }$ does not precede $k$ and the answer span is not longer than 500 characters 

ground_truth: BC5CDR-disease, NCBI-disease, BC5CDR-chem, BC4CHEMD, BC2GM, JNLPBA, LINNAEUS, Species-800

BC5CDR-disease, NCBI-disease, BC5CDR-chem, BC4CHEMD, BC2GM, JNLPBA, LINNAEUS, Species-800