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

Please answer the questions based on the text provided below. Why masking words in the decoder is helpful?
Context 1: Introduction
Text summarization generates summaries from input documents while keeping salient information  It is an important task and can be applied to several real-world applications  Many methods have been proposed to solve the text summarization problem BIBREF0 , BIBREF1 , BIBREF2 , BIBREF3   There are two main text summarization techniques: extractive and abstractive  Extractive summarization generates summary by selecting salient sentences or phrases from the source text, while abstractive methods paraphrase and restructure sentences to compose the summary  We focus on abstractive summarization in this work as it is more flexible and thus can generate more diverse summaries 
Recently, many abstractive approaches are introduced based on neural sequence-to-sequence framework BIBREF4 , BIBREF0 , BIBREF3 , BIBREF5   Based on the sequence-to-sequence model with copy mechanism BIBREF6 , BIBREF0 incorporates a coverage vector to track and control attention scores on source text  BIBREF4 introduce intra-temporal attention processes in the encoder and decoder to address the repetition and incoherent problem 
There are two issues in previous abstractive methods: 1) these methods use left-context-only decoder, thus do not have complete context when predicting each word  2) they do not utilize the pre-trained contextualized language models on the decoder side, so it is more difficult for the decoder to learn summary representations, context interactions and language modeling together 
Recently, BERT has been successfully used in various natural language processing tasks, such as textual entailment, name entity recognition and machine reading comprehensions  In this paper, we present a novel natural language generation model based on pre-trained language models (we use BERT in this work)  As far as we know, this is the first work to extend BERT to the sequence generation task  To address the above issues of previous abstractive methods, in our model, we design a two-stage decoding process to make good use of BERT's context modeling ability  On the first stage, we generate the summary using a left-context-only-decoder  On the second stage, we mask each word of the summary and predict the refined word one-by-one using a refine decoder  To further improve the naturalness of the generated sequence, we cooperate reinforcement objective with the refine decoder 
The main contributions of this work are:
1  We propose a natural language generation model based on BERT, making good use of the pre-trained language model in the encoder and decoder process, and the model can be trained end-to-end without handcrafted features 
2  We design a two-stage decoder process  In this architecture, our model can generate each word of the summary considering both sides' context information 
3  We conduct experiments on the benchmark datasets CNN/Daily Mail and New York Times  Our model achieves a 33 33 average of ROUGE-1, ROUGE-2 and ROUGE-L on the CNN/Daily Mail, which is state-of-the-art  On the New York Times dataset, our model achieves about 5 6% relative improvement over ROUGE-1 
Text Summarization
In this paper, we focus on single-document multi-sentence summarization and propose a supervised abstractive model based on the neural attentive sequence-to-sequence framework which consists of two parts: a neural network for the encoder and another network for the decoder  The encoder encodes the input sequence to intermediate representation and the decoder predicts one word at a time step given the input sequence representation vector and previous decoded output  The goal of the model is to maximize the probability of generating the correct target sequences  In the encoding and generation process, the attention mechanism is used to concentrate on the most important positions of text  The learning objective of most sequence-to-sequence models is to minimize the negative log likelihood of the generated sequence as following equation shows, where $y^*_i$ is the i-th ground-truth summary token 
$$Loss = - \log \sum _{t=1}^N P(y_t^*|y_{<t}^*, X)$$   (Eq  3)
However, with this objective, traditional sequence generation models consider only one direction context in the decoding process, which could cause performance degradation since complete context of one token contains preceding and following tokens, thus feeding only preceded decoded words to the decoder so that the model may generate unnatural sequences  For example, attentive sequence-to-sequence models often generate sequences with repeated phrases which harm the naturalness  Some previous works mitigate this problem by improving the attention calculation process, but in this paper we show that feeding bi-directional context instead of left-only-context can better alleviate this problem 
Text summarization models are usually classified to abstractive and extractive ones  Recently, extractive models like DeepChannel BIBREF8 , rnn-ext+RL BIBREF9 and NeuSUM BIBREF2 achieve higher performances using well-designed structures  For example, DeepChannel propose a salience estimation network and iteratively extract salient sentences  BIBREF16 train a sentence compression model to teach another latent variable extractive model 
Also, several recent works focus on improving abstractive methods  BIBREF3 design a content selector to over-determine phrases in a source document that should be part of the summary  BIBREF11 introduce inconsistency loss to force words in less attended sentences(which determined by extractive model) to have lower generation probabilities  BIBREF5 extend seq2seq model with an information selection network to generate more informative summaries 
Bi-Directional Pre-Trained Context Encoders
Recently, context encoders such as ELMo, GPT, and BERT have been widely used in many NLP tasks  These models are pre-trained on a huge unlabeled corpus and can generate better contextualized token embeddings, thus the approaches built on top of them can achieve better performance 
Since our method is based on BERT, we illustrate the process briefly here  BERT consists of several layers  In each layer there is first a multi-head self-attention sub-layer and then a linear affine sub-layer with the residual connection  In each self-attention sub-layer the attention scores $e_{ij}$ are first calculated as Eq  ( 5 ) () shows, in which $d_e$ is output dimension, and $W^Q, W^K, W^V$ are parameter matrices 
$$&a_{ij} = \cfrac{(h_iW_Q)(h_jW_K)^T}{\sqrt{d_e}}  \\ &e_{ij} = \cfrac{\exp {e_{ij}}}{\sum _{k=1}^N\exp {e_{ik}}} $$   (Eq  5)
Then the output is calculated as Eq  ( 6 ) shows, which is the weighted sum of previous outputs $h$ added by previous output $h_i$   The last layer outputs is context encoding of input sequence 
$$o_i = h_i + \sum _{j=1}^{N} e_{ij}(h_j W_V) $$   (Eq  6)
Despite the wide usage and huge success, there is also a mismatch problem between these pre-trained context encoders and sequence-to-sequence models  The issue is that while using a pre-trained context encoder like GPT or BERT, they model token-level representations by conditioning on both direction context  During pre-training, they are fed with complete sequences  However, with a left-context-only decoder, these pre-trained language models will suffer from incomplete and inconsistent context and thus cannot generate good enough context-aware word representations, especially during the inference process 
Model
In this section, we describe the structure of our model, which learns to generate an abstractive multi-sentence summary from a given source document 
Based on the sequence-to-sequence framework built on top of BERT, we first design a refine decoder at word-level to tackle the two problems described in the above section  We also introduce a discrete objective for the refine decoders to reduce the exposure bias problem  The overall structure of our model is illustrated in Figure 1  
Problem Formulation
We denote the input document as $X = \lbrace x_1, \ldots , x_m\rbrace $ where $x_i \in \mathcal {X}$ represents one source token  The corresponding summary is denoted as $Y = \lbrace y_1, \ldots , y_L\rbrace $ , $L$ represents the summary length 
Given input document $X$ , we first predict the summary draft by a left-context-only decoder, and then using the generated summary draft we can condition on both context sides and refine the content of the summary  The draft will guide and constrain the refine process of summary 
Summary Draft Generation
The summary draft is based on the sequence-to-sequence model  On the encoder side the input document $X$ is encoded into representation vectors $H = \lbrace h_1, \ldots , h_m\rbrace $ , and then fed to the decoder to generate the summary draft $A = \lbrace a_1, \ldots , a_{|a|}\rbrace $  
We simply use BERT as the encoder  It first maps the input sequence to word embeddings and then computes document embeddings as the encoder's output, denoted by following equation 
$$H = BERT(x_1, \ldots , x_m)$$   (Eq  10)
In the draft decoder, we first introduce BERT's word embedding matrix to map the previous summary draft outputs $\lbrace y_1, \ldots , y_{t-1}\rbrace $ into embeddings vectors $\lbrace q_1, \ldots , q_{t-1}\rbrace $ at t-th time step  Note that as the input sequence of the decoder is not complete, we do not use the BERT network to predict the context vectors here 
Then we introduce an $N$ layer Transformer decoder to learn the conditional probability $P(A|H)$   Transformer's decoder-encoder multi-head attention helps the decoder learn soft alignments between summary and source document  At the t-th time step, the draft decoder predicts output probability conditioned on previous outputs and encoder hidden representations as Eq  ( 13 ) shows, in which $q_{<t} = \lbrace q_1, \ldots , q_{t-1}\rbrace $   Each generated sequence will be truncated in the first position of a special token '[PAD]' 
$$&P^{vocab}_t(w) = f_{dec}(q_{<t}, H)  \\ &L_{dec} = \sum _{i=1}^{|a|} -\log P(a_i = y_i^*|a_{< i}, H) $$   (Eq  13)
As Eq  () shows, the decoder's learning objective is to minimize negative likelihood of conditional probability, in which $y_i^*$ is the i-th ground truth word of summary 
However a decoder with this structure is not sufficient enough: if we use the BERT network in this decoder, then during training and inference, in-complete context(part of sentence) is fed into the BERT module, and although we can fine-tune BERT's parameters, the input distribution is quite different from the pre-train process, and thus harms the quality of generated context representations 
If we just use the embedding matrix here, it will be more difficult for the decoder with fresh parameters to learn to model representations as well as vocabulary probabilities, from a relative small corpus compared to BERT's huge pre-training corpus  In a word, the decoder cannot utilize BERT's ability to generate high quality context vectors, which will also harm performance 
This issue exists when using any other contextualized word representations, so we design a refine process to mitigate it in our approach which will be described in the next sub-section 
As some summary tokens are out-of-vocabulary words and occurs in input document, we incorporate copy mechanism BIBREF6 based on the Transformer decoder, we will describe it briefly 
At decoder time step $t$ , we first calculate the attention probability distribution over source document $X$ using the bi-linear dot product of the last layer decoder output of Transformer $o_t$ and the encoder output $h_j$ , as Eq  ( 15 ) () shows 
$$u_t^j =& o_t W_c h_j \\ \alpha _t^j =& \cfrac{\exp {u_t^j}}{\sum _{k=1}^N\exp {u_t^k}} $$   (Eq  15)
We then calculate copying gate $g_t\in [0, 1]$ , which makes a soft choice between selecting from source and generating from vocabulary, $W_c, W_g, b_g$ are parameters:
$$g_t = sigmoid(W_g \cdot [o_t, h] + b_g) $$   (Eq  16)
Using $g_t$ we calculate the weighted sum of copy probability and generation probability to get the final predicted probability of extended vocabulary $\mathcal {V} + \mathcal {X}$ , where $\mathcal {X}$ is the set of out of vocabulary words from the source document  The final probability is calculated as follow:
$$P_t(w) = (1-g_t)P_t^{vocab}(w) + g_t\sum _{i:w_i=w} \alpha _t^i$$   (Eq  17)
Summary Refine Process
The main reason to introduce the refine process is to enhance the decoder using BERT's contextualized representations, so we do not modify the encoder and reuse it during this process 
On the decoder side, we propose a new word-level refine decoder  The refine decoder receives a generated summary draft as input, and outputs a refined summary  It first masks each word in the summary draft one by one, then feeds the draft to BERT to generate context vectors  Finally it predicts a refined summary word using an $N$ layer Transformer decoder which is the same as the draft decoder  At t-th time step the n-th word of input summary is masked, and the decoder predicts the n-th refined word given other words of the summary 
The learning objective of this process is shown in Eq  ( 19 ), $y_i$ is the i-th summary word and $y_{i}^*$ for the ground-truth summary word, and $a_{\ne i} = \lbrace a_1, \ldots , a_{i-1}, a_{i+1}, \ldots , a_{|y|}\rbrace $  
$$L_{refine} = \sum _{i=1}^{|y|} -\log P(y_i = y_i^*|a_{\ne i}, H) $$   (Eq  19)
From the view of BERT or other contextualized embeddings, the refine decoding process provides a more complete input sequence which is consistent with their pre-training processes  Intuitively, this process works as follows: first the draft decoder writes a summary draft based on a document, and then the refine decoder edits the draft  It concentrates on one word at a time, based on the source document as well as other words 
We design the word-level refine decoder because this process is similar to the cloze task in BERT's pre-train process, therefore by using the ability of the contextual language model the decoder can generate more fluent and natural sequences 
The parameters are shared between the draft decoder and refine decoder, as we find that using individual parameters the model's performance degrades a lot  The reason may be that we use teach-forcing during training, and thus the word-level refine decoder learns to predict words given all the other ground-truth words of summary  This objective is similar to the language model's pre-train objective, and is probably not enough for the decoder to learn to generate refined summaries  So in our model all decoders share the same parameters 
Researchers usually use ROUGE as the evaluation metric for summarization, however during sequence-to-sequence model training, the objective is to maximize the log likelihood of generated sequences  This mis-match harms the model's performance, so we add a discrete objective to the model, and optimize it by introducing the policy gradient method  For example, the discrete objective for the summary draft process is as Eq  ( 21 ) shows, where $a^s$ is the draft summary sampled from predicted distribution, and $R(a^s)$ is the reward score compared with the ground-truth summary, we use ROUGE-L in our experiment  To balance between optimizing the discrete objective and generating readable sequences, we mix the discrete objective with maximum-likelihood objective  As Eq  () shows, minimizing $\hat{L}_{dec}$ is the final objective for the draft process, note here $L_{dec}$ is $-logP(a|x)$   In the refine process we introduce similar objectives 
$$L^{rl}_{dec} = R(a^s)\cdot [-\log (P(a^s|x))]  \\ \hat{L}_{dec} = \gamma * L^{rl}_{dec} + (1 - \gamma ) * L_{dec} $$   (Eq  21)
Learning and Inference
During model training, the objective of our model is sum of the two processes, jointly trained using "teacher-forcing" algorithm  During training we feed the ground-truth summary to each decoder and minimize the objective 
$$L_{model} = \hat{L}_{dec} + \hat{L}_{refine}$$   (Eq  23)
At test time, each time step we choose the predicted word by $\hat{y} = argmax_{y^{\prime }} P(y^{\prime }|x)$ , use beam search to generate the draft summaries, and use greedy search to generate the refined summaries 
Settings
In this work, all of our models are built on $BERT_{BASE}$ , although another larger pre-trained model with better performance ( $BERT_{LARGE}$ ) has published but it costs too much time and GPU memory  We use WordPiece embeddings with a 30,000 vocabulary which is the same as BERT  We set the layer of transformer decoders to 12(8 on NYT50), and set the attention heads number to 12(8 on NYT50), set fully-connected sub-layer hidden size to 3072  We train the model using an Adam optimizer with learning rate of $3e-4$ , $\beta _1=0 9$ , $\beta _2=0 999$ and $\epsilon =10^{-9}$ and use a dynamic learning rate during the training process  For regularization, we use dropout BIBREF13 and label smoothing BIBREF14 in our models and set the dropout rate to 0 15, and the label smoothing value to 0 1  We set the RL objective factor $\gamma $ to 0 99 
During training, we set the batch size to 36, and train for 4 epochs(8 epochs for NYT50 since it has many fewer training samples), after training the best model are selected from last 10 models based on development set performance  Due to GPU memory limit, we use gradient accumulation, set accumulate step to 12 and feed 3 samples at each step  We use beam size 4 and length penalty of 1 0 to generate logical form sequences 
We filter repeated tri-grams in beam-search process by setting word probability to zero if it will generate an tri-gram which exists in the existing summary  It is a nice method to avoid phrase repetition since the two datasets seldom contains repeated tri-grams in one summary  We also fine tune the generated sequences using another two simple rules  When there are multi summary sentences with exactly the same content, we keep the first one and remove the other sentences; we also remove sentences with less than 3 words from the result 
To evaluate the performance of our model, we conduct experiments on CNN/Daily Mail dataset, which is a large collection of news articles and modified for summarization  Following BIBREF0 we choose the non-anonymized version of the dataset, which consists of more than 280,000 training samples and 11490 test set samples 
We also conduct experiments on the New York Times(NYT) dataset which also consists of many news articles  The original dataset can be applied here  In our experiment, we follow the dataset splits and other pre-process settings of BIBREF15   We first filter all samples without a full article text or abstract and then remove all samples with summaries shorter than 50 words  Then we choose the test set based on the date of publication(all examples published after January 1, 2007)  The final dataset contains 22,000 training samples and 3,452 test samples and is called NYT50 since all summaries are longer than 50 words 
We tokenize all sequences of the two datasets using the WordPiece tokenizer  After tokenizing, the average article length and summary length of CNN/Daily Mail are 691 and 51, and NYT50's average article length and summary length are 1152 and 75  We truncate the article length to 512, and the summary length to 100 in our experiment(max summary length is set to 150 on NYT50 as its average golden summary length is longer) 
On CNN/Daily Mail dataset, we report the full-length F-1 score of the ROUGE-1, ROUGE-2 and ROUGE-L metrics, calculated using PyRouge package and the Porter stemmer option  On NYT50, following BIBREF4 we evaluate limited length ROUGE recall score(limit the generated summary length to the ground truth length)  We split NYT50 summaries into sentences by semicolons to calculate the ROUGE scores 
Results and Analysis
Table 1 shows the results on CNN/Daily Mail dataset, we compare the performance of many recent approaches with our model  We classify them to two groups based on whether they are extractive or abstractive models  As the last line of the table shows, the ROUGE-1 and ROUGE-2 score of our full model is comparable with DCA, and outperforms on ROUGE-L  Also, compared to extractive models NeuSUM and MASK- $LM^{global}$ , we achieve slight higher ROUGE-1  Except the four scores, our model outperforms these models on all the other scores, and since we have 95% confidence interval of at most $\pm $ 0 20, these improvements are statistically significant 
As the last four lines of Table 1 show, we conduct an ablation study on our model variants to analyze the importance of each component  We use three ablation models for the experiments  One-Stage: A sequence-to-sequence model with copy mechanism based on BERT; Two-Stage: Adding the word-refine decoder to the One-Stage model; Two-Stage + RL: Full model with refine process cooperated with RL objective 
First, we compare the Two-Stage+RL model with Two-Stage ablation, we observe that the full model outperforms by 0 30 on average ROUGE, suggesting that the reinforcement objective helps the model effectively  Then we analyze the effect of refine process by removing word-level refine from the Two-Stage model, we observe that without the refine process the average ROUGE score drops by 1 69  The ablation study shows that each module is necessary for our full model, and the improvements are statistically significant on all metrics 
To evaluate the impact of summary length on model performance, we compare the average rouge score improvements of our model with different length of ground-truth summaries  As the above sub-figure of Figure 2 shows, compared to Pointer-Generator with Coverage, on length interval 40-80(occupies about 70% of test set) the improvements of our model are higher than shorter samples, confirms that with better context representations, in longer documents our model can achieve higher performance 
As the below sub-figure of Figure 2 shows, compared to extractive baseline: Lead-3 BIBREF0 , the advantage of our model will fall when golden summary length is greater than 80  This probably because that we truncate the long documents and golden summaries and cannot get full information, it could also because that the training data in these intervals is too few to train an abstractive model, so simple extractive method will not fall too far behind 
Additional Results on NYT50
Table 2 shows experiments on the NYT50 corpus  Since the short summary samples are filtered, NYT50 has average longer summaries than CNN/Daily Mail  So the model needs to catch long-term dependency of the sequences to generate good summaries 
The first two lines of Table 2 show results of the two baselines introduced by BIBREF15 : these baselines select first n sentences, or select the first k words from the original document  Also we compare performance of our model with two recent models, we see 2 39 ROUGE-1 improvements compared to the ML+RL with intra-attn approach(previous SOTA) carries over to this dataset, which is a large margin  On ROUGE-2, our model also get an improvement of 0 51  The experiment proves that our approach can outperform competitive methods on different data distributions 
Pre-trained language models
Pre-trained word vectors BIBREF17 , BIBREF18 , BIBREF19 have been widely used in many NLP tasks  More recently, pre-trained language models (ELMo, GPT and BERT), have also achieved great success on several NLP problems such as textual entailment, semantic similarity, reading comprehension, and question answering BIBREF20 , BIBREF21 , BIBREF22  
Some recent works also focus on leveraging pre-trained language models in summarization  BIBREF23 pretrain a language model and use it as the sentiment analyser when generating reviews of goods  BIBREF24 train a language model on golden summaries, and then use it on the decoder side to incorporate prior knowledge 
In this work, we use BERT(which is a pre-trained language model using large scale unlabeled data) on the encoder and decoder of a seq2seq model, and by designing a two stage decoding structure we build a competitive model for abstractive text summarization 
Conclusion and Future Work
In this work, we propose a two-stage model based on sequence-to-sequence paradigm  Our model utilize BERT on both encoder and decoder sides, and introduce reinforce objective in learning process  We evaluate our model on two benchmark datasets CNN/Daily Mail and New York Times, the experimental results show that compared to previous systems our approach effectively improves performance 
Although our experiments are conducted on summarization task, our model can be used in most natural language generation tasks, such as machine translation, question generation and paraphrasing  The refine decoder and mixed objective can also be applied on other sequence generation tasks, and we will investigate on them in future work 
Context 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  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
Users of photo-sharing websites such as Flickr often provide short textual descriptions in the form of tags to help others find the images  With the availability of GPS systems in current electronic devices such as smartphones, latitude and longitude coordinates are nowadays commonly made available as well  The tags associated with such georeferenced photos often describe the location where these photos were taken, and Flickr can thus be regarded as a source of environmental information  The use of Flickr for modelling urban environments has already received considerable attention  For instance, various approaches have been proposed for modelling urban regions BIBREF0 , and for identifying points-of-interest BIBREF1 and itineraries BIBREF2 , BIBREF3   However, the usefulness of Flickr for characterizing the natural environment, which is the focus of this paper, is less well-understood 
Many recent studies have highlighted that Flickr tags capture valuable ecological information, which can be used as a complementary source to more traditional sources  To date, however, ecologists have mostly used social media to conduct manual evaluations of image content with little automated exploitation of the associated tags BIBREF4 , BIBREF5 , BIBREF6   One recent exception is BIBREF7 , where bag-of-words representations derived from Flickr tags were found to give promising result for predicting a range of different environemental phenomena 
Our main hypothesis in this paper is that by using vector space embeddings instead of bag-of-words representations, the ecological information which is implicitly captured by Flickr tags can be utilized in a more effective way  Vector space embeddings are representations in which the objects from a given domain are encoded using relatively low-dimensional vectors  They have proven useful in natural language processing, especially for encoding word meaning BIBREF8 , BIBREF9 , and in machine learning more generally  In this paper, we are interested in the use of such representations for modelling geographic locations  Our main motivation for using vector space embeddings is that they allow us to integrate the textual information we get from Flickr with available structured information in a very natural way  To this end, we rely on an adaptation of the GloVe word embedding model BIBREF9 , but rather than learning word vectors, we learn vectors representing locations  Similar to how the representation of a word in GloVe is determined by the context words surrounding it, the representation of a location in our model is determined by the tags of the photos that have been taken near that location  To incorporate numerical features from structured environmental datasets (e g  average temperature), we associate with each such feature a linear mapping that can be used to predict that feature from a given location vector  This is inspired by the fact that salient properties of a given domain can often be modelled as directions in vector space embeddings BIBREF10 , BIBREF11 , BIBREF12   Finally, evidence from categorical datasets (e g  land cover types) is taken into account by requiring that locations belonging to the same category are represented using similar vectors, similar to how semantic types are sometimes modelled in the context of knowledge graph embedding BIBREF13  
While our point-of-departure is a standard word embedding model, we found that the off-the-shelf GloVe model performed surprisingly poorly, meaning that a number of modifications are needed to achieve good results  Our main findings are as follows  First, given that the number of tags associated with a given location can be quite small, it is important to apply some kind of spatial smoothing, i e  the importance of a given tag for a given location should not only depend on the occurrences of the tag at that location, but also on its occurrences at nearby locations  To this end, we use a formulation which is based on spatially smoothed version of pointwise mutual information  Second, given the wide diversity in the kind of information that is covered by Flickr tags, we find that term selection is in some cases critical to obtain vector spaces that capture the relevant aspects of geographic locations  For instance, many tags on Flickr refer to photography related terms, which we would normally not want to affect the vector representation of a given location  Finally, even with these modifications, vector space embeddings learned from Flickr tags alone are sometimes outperformed by bag-of-words representations  However, our vector space embeddings lead to substantially better predictions in cases where structured (scientific) information is also taken into account  In this sense, the main value of using vector space embeddings in this context is not so much about abstracting away from specific tag usages, but rather about the fact that such representations allow us to integrate numerical and categorical features in a much more natural way than is possible with bag-of-words representations 
The remainder of this paper is organized as follows  In the next section, we provide a discussion of existing work  Section SECREF3 then presents our model for embedding geographic locations from Flickr tags and structured data  Next, in Section SECREF4 we provide a detailed discussion about the experimental results  Finally, Section SECREF5 summarizes our conclusions 
Vector space embeddings
The use of low-dimensional vector space embeddings for representing objects has already proven effective in a large number of applications, including natural language processing (NLP), image processing, and pattern recognition  In the context of NLP, the most prominent example is that of word embeddings, which represent word meaning using vectors of typically around 300 dimensions  A large number of different methods for learning such word embeddings have already been proposed, including Skip-gram and the Continuous Bag-of-Words (CBOW) model BIBREF8 , GloVe BIBREF9 , and fastText BIBREF14   They have been applied effectively in many downstream NLP tasks such as sentiment analysis BIBREF15 , part of speech tagging BIBREF16 , BIBREF17 , and text classification BIBREF18 , BIBREF19   The model we consider in this paper builds on GloVe, which was designed to capture linear regularities of word-word co-occurrence  In GloVe, there are two word vectors INLINEFORM0 and INLINEFORM1 for each word in the vocabulary, which are learned by minimizing the following objective: DISPLAYFORM0
where INLINEFORM0 is the number of times that word INLINEFORM1 appears in the context of word INLINEFORM2 , INLINEFORM3 is the vocabulary size, INLINEFORM4 is the target word bias, INLINEFORM5 is the context word bias  The weighting function INLINEFORM6 is used to limit the impact of rare terms  It is defined as 1 if INLINEFORM7 and as INLINEFORM8 otherwise, where INLINEFORM9 is usually fixed to 100 and INLINEFORM10 to 0 75  Intuitively, the target word vectors INLINEFORM11 correspond to the actual word representations which we would like to find, while the context word vectors INLINEFORM12 model how occurrences of INLINEFORM13 in the context of a given word INLINEFORM14 affect the representation of this latter word  In this paper we will use a similar model, which will however be aimed at learning location vectors instead of the target word vectors 
Beyond word embeddings, various methods have been proposed for learning vector space representations from structured data such as knowledge graphs BIBREF20 , BIBREF21 , BIBREF22 , social networks BIBREF23 , BIBREF24 and taxonomies BIBREF25 , BIBREF26   The idea of combining a word embedding model with structured information has also been explored by several authors, for example to improve the word embeddings based on information coming from knowledge graphs BIBREF27 , BIBREF28   Along similar lines, various lexicons have been used to obtain word embeddings that are better suited at modelling sentiment BIBREF15 and antonymy BIBREF29 , among others  The method proposed by BIBREF30 imposes the condition that words that belong to the same semantic category are closer together than words from different categories, which is somewhat similar in spirit to how we will model categorical datasets in our model 
Embeddings for geographic information
The problem of representing geographic locations using embeddings has also attracted some attention  An early example is BIBREF31 , which used principal component analysis and stacked autoencoders to learn low-dimensional vector representations of city neighbourhoods based on census data  They use these representations to predict attributes such as crime, which is not included in the given census data, and find that in most of the considered evaluation tasks, the low-dimensional vector representations lead to more faithful predictions than the original high-dimensional census data 
Some existing works combine word embedding models with geographic coordinates  For example, in BIBREF32 an approach is proposed to learn word embeddings based on the assumption that words which tend to be used in the same geographic locations are likely to be similar  Note that their aim is dual to our aim in this paper: while they use geographic location to learn word vectors, we use textual descriptions to learn vectors representing geographic locations 
Several methods also use word embedding models to learn representations of Points-of-Interest (POIs) that can be used for predicting user visits BIBREF33 , BIBREF34 , BIBREF35   These works use the machinery of existing word embedding models to learn POI representations, intuitively by letting sequences of POI visits by a user play the role of sequences of words in a sentence  In other words, despite the use of word embedding models, many of these approaches do not actually consider any textual information  For example, in BIBREF34 the Skip-gram model is utilized to create a global pattern of users' POIs  Each location was treated as a word and the other locations visited before or after were treated as context words  They then use a pair-wise ranking loss BIBREF36 which takes into account the user's location visit frequency to personalize the location recommendations  The methods of BIBREF34 were extended in BIBREF35 to use a temporal embedding and to take more account of geographic context, in particular the distances between preferred and non-preferred neighboring POIs, to create a “geographically hierarchical pairwise preference ranking model”  Similarly, in BIBREF37 the CBOW model was trained with POI data  They ordered POIs spatially within the traffic-based zones of urban areas  The ordering was used to generate characteristic vectors of POI types  Zone vectors represented by averaging the vectors of the POIs contained in them, were then used as features to predict land use types  In the CrossMap method BIBREF38 they learned embeddings for spatio-temporal hotspots obtained from social media data of locations, times and text  In one form of embedding, intended to enable reconstruction of records, neighbourhood relations in space and time were encoded by averaging hotspots in a target location's spatial and temporal neighborhoods  They also proposed a graph-based embedding method with nodes of location, time and text

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

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

Please answer the questions based on the text provided below. What are the clinical datasets used in the paper?
Context 3:  The concatenation of the location, time and text vectors were then used as features to predict peoples' activities in urban environments  Finally, in BIBREF39 , a method is proposed that uses the Skip-gram model to represent POI types, based on the intuition that the vector representing a given POI type should be predictive of the POI types that found near places of that type 
Our work is different from these studies, as our focus is on representing locations based on a given text description of that location (in the form of Flickr tags), along with numerical and categorical features from scientific datasets 
Analyzing Flickr tags
Many studies have focused on analyzing Flickr tags to extract useful information in domains such as linguistics BIBREF40 , geography BIBREF0 , BIBREF41 , and ecology BIBREF42 , BIBREF7 , BIBREF43   Most closely related to our work, BIBREF7 found that the tags of georeferenced Flickr photos can effectively supplement traditional scientific environmental data in tasks such as predicting climate features, land cover, species occurrence, and human assessments of scenicness  To encode locations, they simply combine a bag-of-words representation of geographically nearby tags with a feature vector that encodes associated structured scientific data  They found that the predictive value of Flickr tags is roughly on a par with that of the scientific datasets, and that combining both types of information leads to significantly better results than using either of them alone  As we show in this paper, however, their straightforward way of combining both information sources, by concatenating the two types of feature vectors, is far from optimal 
Despite the proven importance of Flickr tags, the problem of embedding Flickr tags has so far received very limited attention  To the best of our knowledge, BIBREF44 is the only work that generated embeddings for Flickr tags  However, their focus was on learning embeddings that capture word meaning (being evaluated on word similarity tasks), whereas we use such embeddings as part of our method for representing locations 
Model Description
In this section, we introduce our embedding model, which combines Flickr tags and structured scientific information to represent a set of locations INLINEFORM0   The proposed model has the following form: DISPLAYFORM0
where INLINEFORM0 and INLINEFORM1 are parameters to control the importance of each component in the model  Component INLINEFORM2 will be used to constrain the representation of the locations based on their textual description (i e  Flickr tags), INLINEFORM3 will be used to constrain the representation of the locations based on their numerical features, and INLINEFORM4 will impose the constraint that locations belonging to the same category should be close together in the space  We will discuss each of these components in more detail in the following sections 
Tag Based Location Embedding
Many of the tags associated with Flickr photos describe characteristics of the places where these photos were taken BIBREF45 , BIBREF46 , BIBREF47   For example, tags may correspond to place names (e g  Brussels, England, Scandinavia), landmarks (e g  Eiffel Tower, Empire State Building) or land cover types (e g  mountain, forest, beach)  To allow us to build location models using such tags, we collected the tags and meta-data of 70 million Flickr photos with coordinates in Europe (which is the region our experiments will focus on), all of which were uploaded to Flickr before the end of September 2015  In this section we first explain how tags can be weighted to obtain bag-of-words representations of locations from Flickr  Subsequently we describe a tag selection method, which will allow us to specialize the embedding depending on which aspects of the considered locations are of interest, after which we discuss the actual embedding model 
Tag weighting  Let INLINEFORM0 be a set of geographic locations, each characterized by latitude and longitude coordinates  To generate a bag-of-words representation of a given location, we have to weight the relevance of each tag to that location  To this end, we have followed the weighting scheme from BIBREF7 , which combines a Gaussian kernel (to model spatial proximity) with Positive Pointwise Mutual Information (PPMI) BIBREF48 , BIBREF49  
Let us write INLINEFORM0 for the set of users who have assigned tag INLINEFORM1 to a photo with coordinates near INLINEFORM2   To assess how relevant INLINEFORM3 is to the location INLINEFORM4 , the number of times INLINEFORM5 occurs in photos near INLINEFORM6 is clearly an important criterion  However, rather than simply counting the number of occurrences within some fixed radius, we use a Gaussian kernel to weight the tag occurrences according to their distance from that location: INLINEFORM7
where the threshold INLINEFORM0 is assumed to be fixed, INLINEFORM1 is the location of a Flickr photo, INLINEFORM2 is the Haversine distance, and we will assume that the bandwidth parameter INLINEFORM3 is set to INLINEFORM4   A tag occurrence is counted only once for all photos by the same user at the same location, which is important to reduce the impact of bulk uploading  The value INLINEFORM5 reflects how frequent tag INLINEFORM6 is near location INLINEFORM7 , but it does not yet take into account the total number of tag occurrences near INLINEFORM8 , nor how popular the tag INLINEFORM9 is overall  To measure how strongly tag INLINEFORM10 is associated with location INLINEFORM11 , we use PPMI, which is a commonly used measure of association in natural language processing  However, rather than estimating PPMI scores from term frequencies, we will use the INLINEFORM12 values instead: INLINEFORM13
where: INLINEFORM0
with INLINEFORM0 the set of all tags, and INLINEFORM1 the set of locations 
Tag selection  Inspired by BIBREF50 , we use a term selection method in order to focus on the tags that are most important for the tasks that we want to consider and reduce the impact of tags that might relate only to a given individual or a group of users  In particular, we obtained good results with a method based on Kullback-Leibler (KL) divergence, which is based on BIBREF51   Let INLINEFORM0 be a set of (mutually exclusive) properties of locations in which we are interested (e g  land cover categories)  For the ease of presentation, we will identify INLINEFORM1 with the set of locations that have the corresponding property  Then, we select tags from INLINEFORM2 that maximize the following score: INLINEFORM3
where INLINEFORM0 is the probability that a photo with tag INLINEFORM1 has a location near INLINEFORM2 and INLINEFORM3 is the probability that an arbitrary tag occurrence is assigned to a photo near a location in INLINEFORM4   Since INLINEFORM5 often has to be estimated from a small number of tag occurrences, it is estimated using Bayesian smoothing: INLINEFORM6
where INLINEFORM0 is a parameter controlling the amount of smoothing, which will be tuned in the experiments  On the other hand, for INLINEFORM1 we can simply use a maximum likelihood estimation: INLINEFORM2
Location embedding  We now want to find a vector INLINEFORM0 for each location INLINEFORM1 such that similar locations are represented using similar vectors  To achieve this, we use a close variant of the GloVe model, where tag occurrences are treated as context words of geographic locations  In particular, with each location INLINEFORM2 we associate a vector INLINEFORM3 and with each tag INLINEFORM4 we associate a vector INLINEFORM5 and a bias term INLINEFORM6 , and consider the following objective (which in our full model ( EQREF7 ) will be combined with components that are derived from the structured information): INLINEFORM7
Note how tags play the role of the context words in the GloVe model, while instead of learning target word vectors we now learn location vectors  In contrast to GloVe, our objective does not directly refer to co-occurrence statistics, but instead uses the INLINEFORM0 scores  One important consequence of this is that we can also consider pairs INLINEFORM1 for which INLINEFORM2 does not occur in INLINEFORM3 at all; such pairs are usually called negative examples  While they cannot be used in the standard GloVe model, some authors have already reported that introducing negative examples in variants of GloVe can lead to an improvement BIBREF52   In practice, evaluating the full objective above would not be computationally feasible, as we may need to consider millions of locations and millions of tags  Therefore, rather than considering all tags in INLINEFORM4 for the inner summation, we only consider those tags that appear at least once near location INLINEFORM5 together with a sample of negative examples 
Structured Environmental Data
There is a wide variety of structured data that can be used to describe locations  In this work, we have restricted ourselves to the same datasets as BIBREF7   These include nine (real-valued) numerical features, which are latitude, longitude, elevation, population, and five climate related features (avg  temperature, avg  precipitation, avg  solar radiation, avg  wind speed, and avg  water vapor pressure)  In addition, 180 categorical features were used, which are CORINE land cover classes at level 1 (5 classes), level 2 (15 classes) and level 3 (44 classes) and 116 soil types (SoilGrids)  Note that each location should belong to exactly 4 categories: one CORINE class at each of the three levels and a soil type 
Numerical features  Numerical features can be treated similarly to the tag occurrences, i e  we will assume that the value of a given numerical feature can be predicted from the location vectors using a linear mapping  In particular, for each numerical feature INLINEFORM0 we consider a vector INLINEFORM1 and a bias term INLINEFORM2 , and the following objective: INLINEFORM3
where we write INLINEFORM0 for set of all numerical features and INLINEFORM1 is the value of feature INLINEFORM2 for location INLINEFORM3 , after z-score normalization 
Categorical features  To take into account the categorical features, we impose the constraint that locations belonging to the same category should be close together in the space

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. what are the existing approaches?
Context 3:  To formalize this, we represent each category type INLINEFORM0 as a vector INLINEFORM1 , and consider the following objective: INLINEFORM2
Evaluation Tasks
We will use the method from BIBREF7 as our main baseline  This will allow us to directly evaluate the effectiveness of embeddings for the considered problem, since we have used the same structured datasets and same tag weighting scheme  For this reason, we will also follow their evaluation methodology  In particular, we will consider three evaluation tasks:
Predicting the distribution of 100 species across Europe, using the European network of nature protected sites Natura 2000 dataset as ground truth  For each of these species, a binary classification problem is considered  The set of locations INLINEFORM0 is defined as the 26,425 distinct sites occurring in the dataset 
Predicting soil type, again each time treating the task as a binary classification problem, using the same set of locations INLINEFORM0 as in the species distribution experiments  For these experiments, none of the soil type features are used for generating the embeddings 
Predicting CORINE land cover classes at levels 1, 2 and level 3, each time treating the task as a binary classification problem, using the same set of locations INLINEFORM0 as in the species distribution experiments  For these experiments, none of the CORINE features are used for generating the embeddings 
In addition, we will also consider the following regression tasks:
Predicting 5 climate related features: the average precipitation, temperature, solar radiation, water vapor pressure, and wind speed  We again use the same set of locations INLINEFORM0 as for species distribution in this experiment  None of the climate features is used for constructing the embeddings for this experiment 
Predicting people's subjective opinions of landscape beauty in Britain, using the crowdsourced dataset from the ScenicOrNot website as ground truth  The set INLINEFORM0 is chosen as the set of locations of 191 605 rated locations from the ScenicOrNot dataset for which at least one georeferenced Flickr photo exists within a 1 km radius 
Experimental Setup
In all experiments, we use Support Vector Machines (SVMs) for classification problems and Support Vector Regression (SVR) for regression problems to make predictions from our representations of geographic locations  In both cases, we used the SVM INLINEFORM0 implementation BIBREF53   For each experiment, the set of locations INLINEFORM1 was split into two-thirds for training, one-sixth for testing, and one-sixth for tuning the parameters  All embedding models are learned with Adagrad using 30 iterations  The number of dimensions is chosen for each experiment from INLINEFORM2 based on the tuning data  For the parameters of our model in Equation EQREF7 , we considered values of INLINEFORM3 from {0 1, 0 01, 0 001, 0 0001} and values of INLINEFORM4 from {1, 10, 100, 1000, 10 000, 100 000}  To compute KL divergence, we need to determine a set of classes INLINEFORM5 for each experiment  For classification problems, we can simply consider the given categories, but for the regression problems we need to define such classes by discretizing the numerical values  For the scenicness experiments, we considered scores 3 and 7 as cut-off points, leading to three classes (i e  less than 3, between 3 and 7, and above 7)  Similarly, for each climate related features, we consider two cut-off values for discretization: 5 and 15 for average temperature, 50 and 100 for average precipitation, 10 000 and 17 000 for average solar radiation, 0 7 and 1 for average water vapor pressure, and 3 and 5 for wind speed  The smoothing parameter INLINEFORM6 was selected among INLINEFORM7 based on the tuning data  In all experiments where term selection is used, we select the top 100 000 tags  We fixed the radius INLINEFORM8 at 1km when counting the number of tag occurrences  Finally, we set the number of negative examples as 10 times the number of positive examples for each location, but with a cap at 1000 negative examples in each region for computational reasons  We tune all parameters with respect to the F1 score for the classification tasks, and Spearman INLINEFORM9 for the regression tasks 
Variants and Baseline Methods
We will refer to our model as EGEL (Embedding GEographic Locations), and will consider the following variants  EGEL-Tags only uses the information from the Flickr tags (i e  component INLINEFORM0 ), without using any negative examples and without feature selection  EGEL-Tags+NS is similar to EGEL-Tags but with the addition of negative examples  EGEL-KL(Tags+NS) additionally considers term selection  EGEL-All is our full method, i e  it additionally uses the structured information  We also consider the following baselines  BOW-Tags represents locations using a bag-of-words representation, using the same tag weighting as the embedding model  BOW-KL(Tags) uses the same representation but after term selection, using the same KL-based method as the embedding model  BOW-All combines the bag-of-words representation with the structured information, encoded as proposed in BIBREF7   GloVe uses the objective from the original GloVe model for learning location vectors, i e  this variant differs from EGEL-Tags in that instead of INLINEFORM1 we use the number of co-occurrences of tag INLINEFORM2 near location INLINEFORM3 , measured as INLINEFORM4  
Results and Discussion
We present our results for the binary classification tasks in Tables TABREF23 – TABREF24 in terms of average precision, average recall and macro average F1 score  The results of the regression tasks are reported in Tables TABREF25 and TABREF29 in terms of the mean absolute error between the predicted and actual scores, as well as the Spearman INLINEFORM0 correlation between the rankings induced by both sets of scores  It can be clearly seen from the results that our proposed method (EGEL-All) can effectively integrate Flickr tags with the available structured information  It outperforms the baselines for all the considered tasks  Furthermore, note that the PPMI-based weighting in EGEL-Tags consistently outperforms GloVe and that both the addition of negative examples and term selection lead to further improvements  The use of term selection leads to particularly substantial improvements for the regression problems 
While our experimental results confirm the usefulness of embeddings for predicting environmental features, this is only consistently the case for the variants that use both the tags and the structured datasets  In particular, comparing BOW-Tags with EGEL-Tags, we sometimes see that the former achieves the best results  While this might seem surprising, it is in accordance with the findings in BIBREF54 , BIBREF38 , among others, where it was also found that bag-of-words representations can sometimes lead to surprisingly effective baselines  Interestingly, we note that in all cases where EGEL-KL(Tags+NS) performs worse than BOW-Tags, we also find that BOW-KL(Tags) performs worse than BOW-Tags  This suggests that for these tasks there is a very large variation in the kind of tags that can inform the prediction model, possibly including e g  user-specific tags  Some of the information captured by such highly specific but rare tags is likely to be lost in the embedding 
To further analyze the difference in performance between BoW representations and embeddings, Figure TABREF29 compares the performance of the GloVe model with the bag-of-words model for predicting place scenicness, as a function of the number of tag occurrences at the considered locations  What is clearly noticeable in Figure TABREF29 is that GloVe performs better than the bag-of-words model for large corpora and worse for smaller corpora  This issue has been alleviated in our embedding method by the addition of negative examples 
 Conclusions
In this paper, we have proposed a model to learn geographic location embeddings using Flickr tags, numerical environmental features, and categorical information  The experimental results show that our model can integrate Flickr tags with structured information in a more effective way than existing methods, leading to substantial improvements over baseline methods on various prediction tasks about the natural environment 
Acknowledgments
Shelan Jeawak has been sponsored by HCED Iraq  Steven Schockaert has been supported by ERC Starting Grant 637277 

ground_truth: BOW-Tags, BOW-KL(Tags), BOW-All, GloVe