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 was their performance on emotion detection?
Context 1: Introduction
This work is licenced under a Creative Commons Attribution 4 0 International Licence  Licence details: http://creativecommons org/licenses/by/4 0/
In the spirit of the brevity of social media's messages and reactions, people have got used to express feelings minimally and symbolically, as with hashtags on Twitter and Instagram  On Facebook, people tend to be more wordy, but posts normally receive more simple “likes” than longer comments  Since February 2016, Facebook users can express specific emotions in response to a post thanks to the newly introduced reaction feature (see Section SECREF2 ), so that now a post can be wordlessly marked with an expression of say “joy" or “surprise" rather than a generic “like” 
It has been observed that this new feature helps Facebook to know much more about their users and exploit this information for targeted advertising BIBREF0 , but interest in people's opinions and how they feel isn't limited to commercial reasons, as it invests social monitoring, too, including health care and education BIBREF1   However, emotions and opinions are not always expressed this explicitly, so that there is high interest in developing systems towards their automatic detection  Creating manually annotated datasets large enough to train supervised models is not only costly, but also—especially in the case of opinions and emotions—difficult, due to the intrinsic subjectivity of the task BIBREF2 , BIBREF3   Therefore, research has focused on unsupervised methods enriched with information derived from lexica, which are manually created BIBREF3 , BIBREF4   Since go2009twitter have shown that happy and sad emoticons can be successfully used as signals for sentiment labels, distant supervision, i e  using some reasonably safe signals as proxies for automatically labelling training data BIBREF5 , has been used also for emotion recognition, for example exploiting both emoticons and Twitter hashtags BIBREF6 , but mainly towards creating emotion lexica  mohammad2015using use hashtags, experimenting also with highly fine-grained emotion sets (up to almost 600 emotion labels), to create the large Hashtag Emotion Lexicon  Emoticons are used as proxies also by hallsmarmulti, who use distributed vector representations to find which words are interchangeable with emoticons but also which emoticons are used in a similar context 
We take advantage of distant supervision by using Facebook reactions as proxies for emotion labels, which to the best of our knowledge hasn't been done yet, and we train a set of Support Vector Machine models for emotion recognition  Our models, differently from existing ones, exploit information which is acquired entirely automatically, and achieve competitive or even state-of-the-art results for some of the emotion labels on existing, standard evaluation datasets  For explanatory purposes, related work is discussed further and more in detail when we describe the benchmarks for evaluation (Section SECREF3 ) and when we compare our models to existing ones (Section SECREF5 )  We also explore and discuss how choosing different sets of Facebook pages as training data provides an intrinsic domain-adaptation method 
Facebook reactions as labels
For years, on Facebook people could leave comments to posts, and also “like” them, by using a thumbs-up feature to explicitly express a generic, rather underspecified, approval  A “like” could thus mean “I like what you said", but also “I like that you bring up such topic (though I find the content of the article you linked annoying)" 
In February 2016, after a short trial, Facebook made a more explicit reaction feature available world-wide  Rather than allowing for the underspecified “like” as the only wordless response to a post, a set of six more specific reactions was introduced, as shown in Figure FIGREF1 : Like, Love, Haha, Wow, Sad and Angry  We use such reactions as proxies for emotion labels associated to posts 
We collected Facebook posts and their corresponding reactions from public pages using the Facebook API, which we accessed via the Facebook-sdk python library  We chose different pages (and therefore domains and stances), aiming at a balanced and varied dataset, but we did so mainly based on intuition (see Section SECREF4 ) and with an eye to the nature of the datasets available for evaluation (see Section SECREF5 )  The choice of which pages to select posts from is far from trivial, and we believe this is actually an interesting aspect of our approach, as by using different Facebook pages one can intrinsically tackle the domain-adaptation problem (See Section SECREF6 for further discussion on this)  The final collection of Facebook pages for the experiments described in this paper is as follows: FoxNews, CNN, ESPN, New York Times, Time magazine, Huffington Post Weird News, The Guardian, Cartoon Network, Cooking Light, Home Cooking Adventure, Justin Bieber, Nickelodeon, Spongebob, Disney 
Note that thankful was only available during specific time spans related to certain events, as Mother's Day in May 2016 
For each page, we downloaded the latest 1000 posts, or the maximum available if there are fewer, from February 2016, retrieving the counts of reactions for each post  The output is a JSON file containing a list of dictionaries with a timestamp, the post and a reaction vector with frequency values, which indicate how many users used that reaction in response to the post (Figure FIGREF3 )  The resulting emotion vectors must then be turned into an emotion label 
In the context of this experiment, we made the simple decision of associating to each post the emotion with the highest count, ignoring like as it is the default and most generic reaction people tend to use  Therefore, for example, to the first post in Figure FIGREF3 , we would associate the label sad, as it has the highest score (284) among the meaningful emotions we consider, though it also has non-zero scores for other emotions  At this stage, we didn't perform any other entropy-based selection of posts, to be investigated in future work 
Emotion datasets
Three datasets annotated with emotions are commonly used for the development and evaluation of emotion detection systems, namely the Affective Text dataset, the Fairy Tales dataset, and the ISEAR dataset  In order to compare our performance to state-of-the-art results, we have used them as well  In this Section, in addition to a description of each dataset, we provide an overview of the emotions used, their distribution, and how we mapped them to those we obtained from Facebook posts in Section SECREF7   A summary is provided in Table TABREF8 , which also shows, in the bottom row, what role each dataset has in our experiments: apart from the development portion of the Affective Text, which we used to develop our models (Section SECREF4 ), all three have been used as benchmarks for our evaluation 
Affective Text dataset
Task 14 at SemEval 2007 BIBREF7 was concerned with the classification of emotions and valence in news headlines  The headlines where collected from several news websites including Google news, The New York Times, BBC News and CNN  The used emotion labels were Anger, Disgust, Fear, Joy, Sadness, Surprise, in line with the six basic emotions of Ekman's standard model BIBREF8   Valence was to be determined as positive or negative  Classification of emotion and valence were treated as separate tasks  Emotion labels were not considered as mututally exclusive, and each emotion was assigned a score from 0 to 100  Training/developing data amounted to 250 annotated headlines (Affective development), while systems were evaluated on another 1000 (Affective test)  Evaluation was done using two different methods: a fine-grained evaluation using Pearson's r to measure the correlation between the system scores and the gold standard; and a coarse-grained method where each emotion score was converted to a binary label, and precision, recall, and f-score were computed to assess performance  As it is done in most works that use this dataset BIBREF3 , BIBREF4 , BIBREF9 , we also treat this as a classification problem (coarse-grained)  This dataset has been extensively used for the evaluation of various unsupervised methods BIBREF2 , but also for testing different supervised learning techniques and feature portability BIBREF10  
Fairy Tales dataset
This is a dataset collected by alm2008affect, where about 1,000 sentences from fairy tales (by B  Potter, H C  Andersen and Grimm) were annotated with the same six emotions of the Affective Text dataset, though with different names: Angry, Disgusted, Fearful, Happy, Sad, and Surprised  In most works that use this dataset BIBREF3 , BIBREF4 , BIBREF9 , only sentences where all annotators agreed are used, and the labels angry and disgusted are merged  We adopt the same choices 
ISEAR
The ISEAR (International Survey on Emotion Antecedents and Reactions BIBREF11 , BIBREF12 ) is a dataset created in the context of a psychology project of the 1990s, by collecting questionnaires answered by people with different cultural backgrounds  The main aim of this project was to gather insights in cross-cultural aspects of emotional reactions  Student respondents, both psychologists and non-psychologists, were asked to report situations in which they had experienced all of seven major emotions (joy, fear, anger, sadness, disgust, shame and guilt)  In each case, the questions covered the way they had appraised a given situation and how they reacted  The final dataset contains reports by approximately 3000 respondents from all over the world, for a total of 7665 sentences labelled with an emotion, making this the largest dataset out of the three we use 
Overview of datasets and emotions
We summarise datasets and emotion distribution from two viewpoints  First, because there are different sets of emotions labels in the datasets and Facebook data, we need to provide a mapping and derive a subset of emotions that we are going to use for the experiments  This is shown in Table TABREF8 , where in the “Mapped” column we report the final emotions we use in this paper: anger, joy, sadness, surprise  All labels in each dataset are mapped to these final emotions, which are therefore the labels we use for training and testing our models 
Second, the distribution of the emotions for each dataset is different, as can be seen in Figure FIGREF9  
In Figure FIGREF9 we also provide the distribution of the emotions anger, joy, sadness, surprise per Facebook page, in terms of number of posts (recall that we assign to a post the label corresponding to the majority emotion associated to it, see Section SECREF2 )  We can observe that for example pages about news tend to have more sadness and anger posts, while pages about cooking and tv-shows have a high percentage of joy posts  We will use this information to find the best set of pages for a given target domain (see Section SECREF5 ) 
Model
There are two main decisions to be taken in developing our model: (i) which Facebook pages to select as training data, and (ii) which features to use to train the model, which we discuss below  Specifically, we first set on a subset of pages and then experiment with features  Further exploration of the interaction between choice of pages and choice of features is left to future work, and partly discussed in Section SECREF6   For development, we use a small portion of the Affective data set described in Section SECREF4 , that is the portion that had been released as development set for SemEval's 2007 Task 14 BIBREF7 , which contains 250 annotated sentences (Affective development, Section SECREF4 )  All results reported in this section are on this dataset  The test set of Task 14 as well as the other two datasets described in Section SECREF3 will be used to evaluate the final models (Section SECREF4 ) 
Selecting Facebook pages
Although page selection is a crucial ingredient of this approach, which we believe calls for further and deeper, dedicated investigation, for the experiments described here we took a rather simple approach  First, we selected the pages that would provide training data based on intuition and availability, then chose different combinations according to results of a basic model run on development data, and eventually tested feature combinations, still on the development set 
For the sake of simplicity and transparency, we first trained an SVM with a simple bag-of-words model and default parameters as per the Scikit-learn implementation BIBREF13 on different combinations of pages  Based on results of the attempted combinations as well as on the distribution of emotions in the development dataset (Figure FIGREF9 ), we selected a best model (B-M), namely the combined set of Time, The Guardian and Disney, which yields the highest results on development data  Time and The Guardian perform well on most emotions but Disney helps to boost the performance for the Joy class 
Features
In selecting appropriate features, we mainly relied on previous work and intuition  We experimented with different combinations, and all tests were still done on Affective development, using the pages for the best model (B-M) described above as training data  Results are in Table TABREF20   Future work will further explore the simultaneous selection of features and page combinations 
We use a set of basic text-based features to capture the emotion class  These include a tf-idf bag-of-words feature, word (2-3) and character (2-5) ngrams, and features related to the presence of negation words, and to the usage of punctuation 
This feature is used in all unsupervised models as a source of information, and we mainly include it to assess its contribution, but eventually do not use it in our final model 
We used the NRC10 Lexicon because it performed best in the experiments by BIBREF10 , which is built around the emotions anger, anticipation, disgust, fear, joy, sadness, and surprise, and the valence values positive and negative  For each word in the lexicon, a boolean value indicating presence or absence is associated to each emotion  For a whole sentence, a global score per emotion can be obtained by summing the vectors for all content words of that sentence included in the lexicon, and used as feature 
As additional feature, we also included Word Embeddings, namely distributed representations of words in a vector space, which have been exceptionally successful in boosting performance in a plethora of NLP tasks  We use three different embeddings:
Google embeddings: pre-trained embeddings trained on Google News and obtained with the skip-gram architecture described in BIBREF14   This model contains 300-dimensional vectors for 3 million words and phrases 
Facebook embeddings: embeddings that we trained on our scraped Facebook pages for a total of 20,000 sentences  Using the gensim library BIBREF15 , we trained the embeddings with the following parameters: window size of 5, learning rate of 0 01 and dimensionality of 100  We filtered out words with frequency lower than 2 occurrences 
Retrofitted embeddings: Retrofitting BIBREF16 has been shown as a simple but efficient way of informing trained embeddings with additional information derived from some lexical resource, rather than including it directly at the training stage, as it's done for example to create sense-aware BIBREF17 or sentiment-aware BIBREF18 embeddings  In this work, we retrofit general embeddings to include information about emotions, so that emotion-similar words can get closer in space  Both the Google as well as our Facebook embeddings were retrofitted with lexical information obtained from the NRC10 Lexicon mentioned above, which provides emotion-similarity for each token  Note that differently from the previous two types of embeddings, the retrofitted ones do rely on handcrafted information in the form of a lexical resource 
Results on development set
We report precision, recall, and f-score on the development set  The average f-score is reported as micro-average, to better account for the skewed distribution of the classes as well as in accordance to what is usually reported for this task BIBREF19  
From Table TABREF20 we draw three main observations  First, a simple tf-idf bag-of-word mode works already very well, to the point that the other textual and lexicon-based features don't seem to contribute to the overall f-score (0 368), although there is a rather substantial variation of scores per class  Second, Google embeddings perform a lot better than Facebook embeddings, and this is likely due to the size of the corpus used for training  Retrofitting doesn't seem to help at all for the Google embeddings, but it does boost the Facebook embeddings, leading to think that with little data, more accurate task-related information is helping, but corpus size matters most  Third, in combination with embeddings, all features work better than just using tf-idf, but removing the Lexicon feature, which is the only one based on hand-crafted resources, yields even better results  Then our best model (B-M) on development data relies entirely on automatically obtained information, both in terms of training data as well as features 
Results
In Table TABREF26 we report the results of our model on the three datasets standardly used for the evaluation of emotion classification, which we have described in Section SECREF3  
Our B-M model relies on subsets of Facebook pages for training, which were chosen according to their performance on the development set as well as on the observation of emotions distribution on different pages and in the different datasets, as described in Section SECREF4   The feature set we use is our best on the development set, namely all the features plus Google-based embeddings, but excluding the lexicon  This makes our approach completely independent of any manual annotation or handcrafted resource  Our model's performance is compared to the following systems, for which results are reported in the referred literature  Please note that no other existing model was re-implemented, and results are those reported in the respective papers 
Discussion, conclusions and future work
We have explored the potential of using Facebook reactions in a distant supervised setting to perform emotion classification  The evaluation on standard benchmarks shows that models trained as such, especially when enhanced with continuous vector representations, can achieve competitive results without relying on any handcrafted resource  An interesting aspect of our approach is the view to domain adaptation via the selection of Facebook pages to be used as training data 
We believe that this approach has a lot of potential, and we see the following directions for improvement  Feature-wise, we want to train emotion-aware embeddings, in the vein of work by tang:14, and iacobacci2015sensembed  Retrofitting FB-embeddings trained on a larger corpus might also be successful, but would rely on an external lexicon 
The largest room for yielding not only better results but also interesting insights on extensions of this approach lies in the choice of training instances, both in terms of Facebook pages to get posts from, as well as in which posts to select from the given pages  For the latter, one could for example only select posts that have a certain length, ignore posts that are only quotes or captions to images, or expand posts by including content from linked html pages, which might provide larger and better contexts BIBREF23   Additionally, and most importantly, one could use an entropy-based measure to select only posts that have a strong emotion rather than just considering the majority emotion as training label  For the former, namely the choice of Facebook pages, which we believe deserves the most investigation, one could explore several avenues, especially in relation to stance-based issues BIBREF24   In our dataset, for example, a post about Chile beating Colombia in a football match during the Copa America had very contradictory reactions, depending on which side readers would cheer for  Similarly, the very same political event, for example, would get very different reactions from readers if it was posted on Fox News or The Late Night Show, as the target audience is likely to feel very differently about the same issue  This also brings up theoretical issues related more generally to the definition of the emotion detection task, as it's strongly dependent on personal traits of the audience  Also, in this work, pages initially selected on availability and intuition were further grouped into sets to make training data according to performance on development data, and label distribution  Another criterion to be exploited would be vocabulary overlap between the pages and the datasets 
Lastly, we could develop single models for each emotion, treating the problem as a multi-label task  This would even better reflect the ambiguity and subjectivity intrinsic to assigning emotions to text, where content could be at same time joyful or sad, depending on the reader 
Acknowledgements
In addition to the anonymous reviewers, we want to thank Lucia Passaro and Barbara Plank for insightful discussions, and for providing comments on draft versions of this paper 
Context 2: Introduction
The automatic processing of medical texts and documents plays an increasingly important role in the recent development of the digital health area  To enable dedicated Natural Language Processing (NLP) that is highly accurate with respect to medically relevant categories, manually annotated data from this domain is needed  One category of high interest and relevance are medical entities  Only very few annotated corpora in the medical domain exist  Many of them focus on the relation between chemicals and diseases or proteins and diseases, such as the BC5CDR corpus BIBREF0, the Comparative Toxicogenomics Database BIBREF1, the FSU PRotein GEne corpus BIBREF2 or the ADE (adverse drug effect) corpus BIBREF3  The NCBI Disease Corpus BIBREF4 contains condition mention annotations along with annotations of symptoms  Several new corpora of annotated case reports were made available recently  grouin-etal-2019-clinical presented a corpus with medical entity annotations of clinical cases written in French, copdPhenotype presented a corpus focusing on phenotypic information for chronic obstructive pulmonary disease while 10 1093/database/bay143 presented a corpus focusing on identifying main finding sentences in case reports 
The corpus most comparable to ours is the French corpus of clinical case reports by grouin-etal-2019-clinical  Their annotations are based on UMLS semantic types  Even though there is an overlap in annotated entities, semantic classes are not the same  Lab results are subsumed under findings in our corpus and are not annotated as their own class  Factors extend beyond gender and age and describe any kind of risk factor that contributes to a higher probability of having a certain disease  Our corpus includes additional entity types  We annotate conditions, findings (including medical findings such as blood values), factors, and also modifiers which indicate the negation of other entities as well as case entities, i  e , entities specific to one case report  An overview is available in Table TABREF3 
A Corpus of Medical Case Reports with Medical Entity Annotation ::: Annotation tasks
Case reports are standardized in the CARE guidelines BIBREF5  They represent a detailed description of the symptoms, signs, diagnosis, treatment, and follow-up of an individual patient  We focus on documents freely available through PubMed Central (PMC)  The presentation of the patient's case can usually be found in a dedicated section or the abstract  We perform a manual annotation of all mentions of case entities, conditions, findings, factors and modifiers  The scope of our manual annotation is limited to the presentation of a patient's signs and symptoms  In addition, we annotate the title of the case report 
A Corpus of Medical Case Reports with Medical Entity Annotation ::: Annotation Guidelines
We annotate the following entities:
case entity marks the mention of a patient  A case report can contain more than one case description  Therefore, all the findings, factors and conditions related to one patient are linked to the respective case entity  Within the text, this entity is often represented by the first mention of the patient and overlaps with the factor annotations which can, e  g , mark sex and age (cf  Figure FIGREF12) 
condition marks a medical disease such as pneumothorax or dislocation of the shoulder 
factor marks a feature of a patient which might influence the probability for a specific diagnosis  It can be immutable (e  g , sex and age), describe a specific medical history (e  g , diabetes mellitus) or a behaviour (e  g , smoking) 
finding marks a sign or symptom a patient shows  This can be visible (e  g , rash), described by a patient (e  g , headache) or measurable (e  g , decreased blood glucose level) 
negation modifier explicitly negate the presence of a certain finding usually setting the case apart from common cases 
We also annotate relations between these entities, where applicable  Since we work on case descriptions, the anchor point of these relations is the case that is described  The following relations are annotated:
has relations exist between a case entity and factor, finding or condition entities 
modifies relations exist between negation modifiers and findings 
causes relations exist between conditions and findings 
Example annotations are shown in Figure FIGREF16 
A Corpus of Medical Case Reports with Medical Entity Annotation ::: Annotators
We asked medical doctors experienced in extracting knowledge related to medical entities from texts to annotate the entities described above  Initially, we asked four annotators to test our guidelines on two texts  Subsequently, identified issues were discussed and resolved  Following this pilot annotation phase, we asked two different annotators to annotate two case reports according to our guidelines  The same annotators annotated an overall collection of 53 case reports 
Inter-annotator agreement is calculated based on two case reports  We reach a Cohen's kappa BIBREF6 of 0 68  Disagreements mainly appear for findings that are rather unspecific such as She no longer eats out with friends which can be seen as a finding referring to “avoidance behaviour” 
A Corpus of Medical Case Reports with Medical Entity Annotation ::: Annotation Tools and Format
The annotation was performed using WebAnno BIBREF7, a web-based tool for linguistic annotation  The annotators could choose between a pre-annotated version or a blank version of each text  The pre-annotated versions contained suggested entity spans based on string matches from lists of conditions and findings synonym lists  Their quality varied widely throughout the corpus  The blank version was preferred by the annotators  We distribute the corpus in BioC JSON format  BioC was chosen as it allows us to capture the complexities of the annotations in the biomedical domain  It represented each documents properties ranging from full text, individual passages/sentences along with captured annotations and relationships in an organized manner  BioC is based on character offsets of annotations and allows the stacking of different layers 
A Corpus of Medical Case Reports with Medical Entity Annotation ::: Corpus Overview
The corpus consists of 53 documents, which contain an average number of 156 1 sentences per document, each with 19 55 tokens on average  The corpus comprises 8,275 sentences and 167,739 words in total  However, as mentioned above, only case presentation sections, headings and abstracts are annotated  The numbers of annotated entities are summarized in Table TABREF24 
Findings are the most frequently annotated type of entity  This makes sense given that findings paint a clinical picture of the patient's condition  The number of tokens per entity ranges from one token for all types to 5 tokens for cases (average length 3 1), nine tokens for conditions (average length 2 0), 16 tokens for factors (average length 2 5), 25 tokens for findings (average length 2 6) and 18 tokens for modifiers (average length 1 4) (cf  Table TABREF24)  Examples of rather long entities are given in Table TABREF25 
Entities can appear in a discontinuous way  We model this as a relation between two spans which we call “discontinuous” (cf  Figure FIGREF26)  Especially findings often appear as discontinuous entities, we found 543 discontinuous finding relations  The numbers for conditions and factors are lower with seven and two, respectively  Entities can also be nested within one another  This happens either when the span of one annotation is completely embedded in the span of another annotation (fully-nested; cf  Figure FIGREF12), or when there is a partial overlapping between the spans of two different entities (partially-nested; cf  Figure FIGREF12)  There is a high number of inter-sentential relations in the corpus (cf  Table TABREF27)  This can be explained by the fact that the case entity occurs early in each document; furthermore, it is related to finding and factor annotations that are distributed across different sentences 
The most frequently annotated relation in our corpus is the has-relation between a case entity and the findings related to that case  This correlates with the high number of finding entities  The relations contained in our corpus are summarized in Table TABREF27 
Baseline systems for Named Entity Recognition in medical case reports
We evaluate the corpus using Named Entity Recognition (NER), i  e , the task of finding mentions of concepts of interest in unstructured text  We focus on detecting cases, conditions, factors, findings and modifiers in case reports (cf  Section SECREF6)  We approach this as a sequence labeling problem  Four systems were developed to offer comparable robust baselines 
The original documents are pre-processed (sentence splitting and tokenization with ScispaCy)  We do not perform stop word removal or lower-casing of the tokens  The BIO labeling scheme is used to capture the order of tokens belonging to the same entity type and enable span-level detection of entities  Detection of nested and/or discontinuous entities is not supported  The annotated corpus is randomized and split in five folds using scikit-learn BIBREF9  Each fold has a train, test and dev split with the test split defined as  15% of the train split  This ensures comparability between the presented systems 
Baseline systems for Named Entity Recognition in medical case reports ::: Conditional Random Fields
Conditional Random Fields (CRF) BIBREF10 are a standard approach when dealing with sequential data in the context of sequence labeling  We use a combination of linguistic and semantic features, with a context window of size five, to describe each of the tokens and the dependencies between them  Hyper-parameter optimization is performed using randomized search and cross validation  Span-based F1 score is used as the optimization metric 
Baseline systems for Named Entity Recognition in medical case reports ::: BiLSTM-CRF
Prior to the emergence of deep neural language models, BiLSTM-CRF models BIBREF11 had achieved state-of-the-art results for the task of sequence labeling  We use a BiLSTM-CRF model with both word-level and character-level input  BioWordVec BIBREF12 pre-trained word embeddings are used in the embedding layer for the input representation  A bidirectional LSTM layer is applied to a multiplication of the two input representations  Finally, a CRF layer is applied to predict the sequence of labels  Dropout and L1/L2 regularization is used where applicable  He (uniform) initialization BIBREF13 is used to initialize the kernels of the individual layers  As the loss metric, CRF-based loss is used, while optimizing the model based on the CRF Viterbi accuracy  Additionally, span-based F1 score is used to serialize the best performing model  We train for a maximum of 100 epochs, or until an early stopping criterion is reached (no change in validation loss value grater than 0 01 for ten consecutive epochs)  Furthermore, Adam BIBREF14 is used as the optimizer  The learning rate is reduced by a factor of 0 3 in case no significant increase of the optimization metric is achieved in three consecutive epochs 
Baseline systems for Named Entity Recognition in medical case reports ::: Multi-Task Learning
Multi-Task Learning (MTL) BIBREF15 has become popular with the progress in deep learning  This model family is characterized by simultaneous optimization of multiple loss functions and transfer of knowledge achieved this way  The knowledge is transferred through the use of one or multiple shared layers  Through finding supporting patterns in related tasks, MTL provides better generalization on unseen cases and the main tasks we are trying to solve 
We rely on the model presented by bekoulis2018joint and reuse the implementation provided by the authors  The model jointly trains two objectives supported by the dataset: the main task of NER and a supporting task of Relation Extraction (RE)  Two separate models are developed for each of the tasks  The NER task is solved with the help of a BiLSTM-CRF model, similar to the one presented in Section SECREF32 The RE task is solved by using a multi-head selection approach, where each token can have none or more relationships to in-sentence tokens  Additionally, this model also leverages the output of the NER branch model (the CRF prediction) to learn label embeddings  Shared layers consist of a concatenation of word and character embeddings followed by two bidirectional LSTM layers  We keep most of the parameters suggested by the authors and change (1) the number of training epochs to 100 to allow the comparison to other deep learning approaches in this work, (2) use label embeddings of size 64, (3) allow gradient clipping and (4) use $d=0 8$ as the pre-trained word embedding dropout and $d=0 5$ for all other dropouts  $\eta =1^{-3}$ is used as the learning rate with the Adam optimizer and tanh activation functions across layers  Although it is possible to use adversarial training BIBREF16, we omit from using it  We also omit the publication of results for the task of RE as we consider it to be a supporting task and no other competing approaches have been developed 
Baseline systems for Named Entity Recognition in medical case reports ::: BioBERT
Deep neural language models have recently evolved to a successful method for representing text  In particular, Bidirectional Encoder Representations from Transformers (BERT) outperformed previous state-of-the-art methods by a large margin on various NLP tasks BIBREF17  For our experiments, we use BioBERT, an adaptation of BERT for the biomedical domain, pre-trained on PubMed abstracts and PMC full-text articles BIBREF18  The BERT architecture for deriving text representations uses 12 hidden layers, consisting of 768 units each  For NER, token level BIO-tag probabilities are computed with a single output layer based on the representations from the last layer of BERT  We fine-tune the model on the entity recognition task during four training epochs with batch size $b=32$, dropout probability $d=0 1$ and learning rate $\eta =2^{-5}$  These hyper-parameters are proposed by Devlin2018 for BERT fine-tuning 
Baseline systems for Named Entity Recognition in medical case reports ::: Evaluation
To evaluate the performance of the four systems, we calculate the span-level precision (P), recall (R) and F1 scores, along with corresponding micro and macro scores  The reported values are shown in Table TABREF29 and are averaged over five folds, utilising the seqeval framework 
With a macro avg  F1-score of 0 59, MTL achieves the best result with a significant margin compared to CRF, BiLSTM-CRF and BERT  This confirms the usefulness of jointly training multiple objectives (minimizing multiple loss functions), and enabling knowledge transfer, especially in a setting with limited data (which is usually the case in the biomedical NLP domain)  This result also suggest the usefulness of BioBERT for other biomedical datasets as reported by Lee2019  Despite being a rather standard approach, CRF outperforms the more elaborated BiLSTM-CRF, presumably due to data scarcity and class imbalance  We hypothesize that an increase in training data would yield better results for BiLSTM-CRF but not outperform transfer learning approach of MTL (or even BioBERT)  In contrast to other common NER corpora, like CoNLL 2003, even the best baseline system only achieves relatively low scores  This outcome is due to the inherent difficulty of the task (annotators are experienced medical doctors) and the small number of training samples 
Conclusion
We present a new corpus, developed to facilitate the processing of case reports  The corpus focuses on five distinct entity types: cases, conditions, factors, findings and modifiers  Where applicable, relationships between entities are also annotated  Additionally, we annotate discontinuous entities with a special relationship type (discontinuous)  The corpus presented in this paper is the very first of its kind and a valuable addition to the scarce number of corpora available in the field of biomedical NLP  Its complexity, given the discontinuous nature of entities and a high number of nested and multi-label entities, poses new challenges for NLP methods applied for NER and can, hence, be a valuable source for insights into what entities “look like in the wild”  Moreover, it can serve as a playground for new modelling techniques such as the resolution of discontinuous entities as well as multi-task learning given the combination of entities and their relations  We provide an evaluation of four distinct NER systems that will serve as robust baselines for future work but which are, as of yet, unable to solve all the complex challenges this dataset holds  A functional service based on the presented corpus is currently being integrated, as a NER service, in the QURATOR platform BIBREF20 
Acknowledgments
The research presented in this article is funded by the German Federal Ministry of Education and Research (BMBF) through the project QURATOR (Unternehmen Region, Wachstumskern, grant no  03WKDA1A), see http://qurator ai  We want to thank our medical experts for their help annotating the data set, especially Ashlee Finckh and Sophie Klopfenstein 

ground_truth: Answer with content missing: (Table 3) Best author's model B-M average micro f-score is 0.409, 0.459, 0.411 on Affective, Fairy Tales and ISEAR datasets 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. How large is the corpus?
Context 4: Introduction
There is a recent spark of interest in the task of Question Answering (QA) over unstructured textual data, also referred to as Machine Reading Comprehension (MRC)  This is mostly due to wide-spread success of advances in various facets of deep learning related research, such as novel architectures BIBREF0, BIBREF1 that allow for efficient optimisation of neural networks consisting of multiple layers, hardware designed for deep learning purposes and software frameworks BIBREF2, BIBREF3 that allow efficient development and testing of novel approaches  These factors enable researchers to produce models that are pre-trained on large scale corpora and provide contextualised word representations BIBREF4 that are shown to be a vital component towards solutions for a variety of natural language understanding tasks, including MRC BIBREF5  Another important factor that led to the recent success in MRC-related tasks is the widespread availability of various large datasets, e g , SQuAD BIBREF6, that provide sufficient examples for optimising statistical models  The combination of these factors yields notable results, even surpassing human performance BIBREF7 
MRC is a generic task format that can be used to probe for various natural language understanding capabilities BIBREF8  Therefore it is crucially important to establish a rigorous evaluation methodology in order to be able to draw reliable conclusions from conducted experiments  While increasing effort is put into the evaluation of novel architectures, such as keeping the evaluation data from public access to prevent unintentional overfitting to test data, performing ablation and error studies and introducing novel metrics BIBREF9, surprisingly little is done to establish the quality of the data itself  Additionally, recent research arrived at worrisome findings: the data of those gold standards, which is usually gathered involving a crowd-sourcing step, suffers from flaws in design BIBREF10 or contains overly specific keywords BIBREF11  Furthermore, these gold standards contain “annotation artefacts”, cues that lead models into focusing on superficial aspects of text, such as lexical overlap and word order, instead of actual language understanding BIBREF12, BIBREF13  These weaknesses cast some doubt on whether the data can reliably evaluate the reading comprehension performance of the models they evaluate, i e  if the models are indeed being assessed for their capability to read 
Figure FIGREF3 shows an example from HotpotQA BIBREF14, a dataset that exhibits the last kind of weakness mentioned above, i e , the presence of unique keywords in both the question and the passage (in close proximity to the expected answer) 
An evaluation methodology is vital to the fine-grained understanding of challenges associated with a single gold standard, in order to understand in greater detail which capabilities of MRC models it evaluates  More importantly, it allows to draw comparisons between multiple gold standards and between the results of respective state-of-the-art models that are evaluated on them 
In this work, we take a step back and propose a framework to systematically analyse MRC evaluation data, typically a set of questions and expected answers to be derived from accompanying passages  Concretely, we introduce a methodology to categorise the linguistic complexity of the textual data and the reasoning and potential external knowledge required to obtain the expected answer  Additionally we propose to take a closer look at the factual correctness of the expected answers, a quality dimension that appears under-explored in literature 
We demonstrate the usefulness of the proposed framework by applying it to precisely describe and compare six contemporary MRC datasets  Our findings reveal concerns about their factual correctness, the presence of lexical cues that simplify the task of reading comprehension and the lack of semantic altering grammatical modifiers  We release the raw data comprised of 300 paragraphs, questions and answers richly annotated under the proposed framework as a resource for researchers developing natural language understanding models and datasets to utilise further 
To the best of our knowledge this is the first attempt to introduce a common evaluation methodology for MRC gold standards and the first across-the-board qualitative evaluation of MRC datasets with respect to the proposed categories 
Framework for MRC Gold Standard Analysis ::: Problem definition
We define the task of machine reading comprehension, the target application of the proposed methodology as follows: Given a paragraph $P$ that consists of tokens (words) $p_1, \ldots , p_{n_P}$ and a question $Q$ that consists of tokens $q_1 \ldots q_{n_Q}$, the goal is to retrieve an answer $A$ with tokens $a_1 \ldots a_{n_A}$  $A$ is commonly constrained to be one of the following cases BIBREF15, illustrated in Figure FIGREF9:
Multiple choice, where the goal is to predict $A$ from a given set of choices $\mathcal {A}$ 
Cloze-style, where $S$ is a sentence, and $A$ and $Q$ are obtained by removing a sequence of words such that $Q = S - A$  The task is to fill in the resulting gap in $Q$ with the expected answer $A$ to form $S$ 
Span, where is a continuous subsequence of tokens from the paragraph ($A \subseteq P$)  Flavours include multiple spans as the correct answer or $A \subseteq Q$ 
Free form, where $A$ is an unconstrained natural language string 
A gold standard $G$ is composed of $m$ entries $(Q_i, A_i, P_i)_{i\in \lbrace 1,\ldots , m\rbrace }$ 
The performance of an approach is established by comparing its answer predictions $A^*_{i}$ on the given input $(Q_i, T_i)$ (and $\mathcal {A}_i$ for the multiple choice setting) against the expected answer $A_i$ for all $i\in \lbrace 1,\ldots , m\rbrace $ under a performance metric  Typical performance metrics are exact match (EM) or accuracy, i e  the percentage of exactly predicted answers, and the F1 score – the harmonic mean between the precision and the recall of the predicted tokens compared to expected answer tokens  The overall F1 score can either be computed by averaging the F1 scores for every instance or by first averaging the precision and recall and then computing the F1 score from those averages (macro F1)  Free-text answers, meanwhile, are evaluated by means of text generation and summarisation metrics such as BLEU BIBREF16 or ROUGE-L BIBREF17 
Framework for MRC Gold Standard Analysis ::: Dimensions of Interest
In this section we describe a methodology to categorise gold standards according to linguistic complexity, required reasoning and background knowledge, and their factual correctness  Specifically, we use those dimensions as high-level categories of a qualitative annotation schema for annotating question, expected answer and the corresponding context  We further enrich the qualitative annotations by a metric based on lexical cues in order to approximate a lower bound for the complexity of the reading comprehension task  By sampling entries from each gold standard and annotating them, we obtain measurable results and thus are able to make observations about the challenges present in that gold standard data 
Framework for MRC Gold Standard Analysis ::: Dimensions of Interest ::: Problem setting
We are interested in different types of the expected answer  We differentiate between Span, where an answer is a continuous span taken from the passage, Paraphrasing, where the answer is a paraphrase of a text span, Unanswerable, where there is no answer present in the context, and Generated, if it does not fall into any of the other categories  It is not sufficient for an answer to restate the question or combine multiple Span or Paraphrasing answers to be annotated as Generated  It is worth mentioning that we focus our investigations on answerable questions  For a complementary qualitative analysis that categorises unanswerable questions, the reader is referred to Yatskar2019 
Furthermore, we mark a sentence as Supporting Fact if it contains evidence required to produce the expected answer, as they are used further in the complexity analysis 
Framework for MRC Gold Standard Analysis ::: Dimensions of Interest ::: Factual Correctness
An important factor for the quality of a benchmark is its factual correctness, because on the one hand, the presence of factually wrong or debatable examples introduces an upper bound for the achievable performance of models on those gold standards  On the other hand, it is hard to draw conclusions about the correctness of answers produced by a model that is evaluated on partially incorrect data 
One way by which developers of modern crowd-sourced gold standards ensure quality is by having the same entry annotated by multiple workers BIBREF18 and keeping only those with high agreement  We investigate whether this method is enough to establish a sound ground truth answer that is unambiguously correct  Concretely we annotate an answer as Debatable when the passage features multiple plausible answers, when multiple expected answers contradict each other, or an answer is not specific enough with respect to the question and a more specific answer is present  We annotate an answer as Wrong when it is factually wrong and a correct answer is present in the context 
Framework for MRC Gold Standard Analysis ::: Dimensions of Interest ::: Required Reasoning
It is important to understand what types of reasoning the benchmark evaluates, in order to be able to accredit various reasoning capabilities to the models it evaluates  Our proposed reasoning categories are inspired by those found in scientific question answering literature BIBREF19, BIBREF20, as research in this area focuses on understanding the required reasoning capabilities  We include reasoning about the Temporal succession of events, Spatial reasoning about directions and environment, and Causal reasoning about the cause-effect relationship between events  We further annotate (multiple-choice) answers that can only be answered By Exclusion of every other alternative 
We further extend the reasoning categories by operational logic, similar to those required in semantic parsing tasks BIBREF21, as solving those tasks typically requires “multi-hop” reasoning BIBREF14, BIBREF22  When an answer can only be obtained by combining information from different sentences joined by mentioning a common entity, concept, date, fact or event (from here on called entity), we annotate it as Bridge  We further annotate the cases, when the answer is a concrete entity that satisfies a Constraint specified in the question, when it is required to draw a Comparison of multiple entities' properties or when the expected answer is an Intersection of their properties (e g  “What do Person A and Person B have in common?”)
We are interested in the linguistic reasoning capabilities probed by a gold standard, therefore we include the appropriate category used by Wang2019  Specifically, we annotate occurrences that require understanding of Negation, Quantifiers (such as “every”, “some”, or “all”), Conditional (“if    then”) statements and the logical implications of Con-/Disjunction (i e  “and” and “or”) in order to derive the expected answer 
Finally, we investigate whether arithmetic reasoning requirements emerge in MRC gold standards as this can probe for reasoning that is not evaluated by simple answer retrieval BIBREF23  To this end, we annotate the presence of of Addition and Subtraction, answers that require Ordering of numerical values, Counting and Other occurrences of simple mathematical operations 
An example can exhibit multiple forms of reasoning  Notably, we do not annotate any of the categories mentioned above if the expected answer is directly stated in the passage  For example, if the question asks “How many total points were scored in the game?” and the passage contains a sentence similar to “The total score of the game was 51 points”, it does not require any reasoning, in which case we annotate it as Retrieval 
Framework for MRC Gold Standard Analysis ::: Dimensions of Interest ::: Knowledge
Worthwhile knowing is whether the information presented in the context is sufficient to answer the question, as there is an increase of benchmarks deliberately designed to probe a model's reliance on some sort of background knowledge BIBREF24  We seek to categorise the type of knowledge required  Similar to Wang2019, on the one hand we annotate the reliance on factual knowledge, that is (Geo)political/Legal, Cultural/Historic, Technical/Scientific and Other Domain Specific knowledge about the world that can be expressed as a set of facts  On the other hand, we denote Intuitive knowledge requirements, which is challenging to express as a set of facts, such as the knowledge that a parenthetic numerical expression next to a person's name in a biography usually denotes his life span 
Framework for MRC Gold Standard Analysis ::: Dimensions of Interest ::: Linguistic Complexity
Another dimension of interest is the evaluation of various linguistic capabilities of MRC models BIBREF25, BIBREF26, BIBREF27  We aim to establish which linguistic phenomena are probed by gold standards and to which degree  To that end, we draw inspiration from the annotation schema used by Wang2019, and adapt it around lexical semantics and syntax 
More specifically, we annotate features that introduce variance between the supporting facts and the question  With regard to lexical semantics, we focus on the use of redundant words that do not alter the meaning of a sentence for the task of retrieving the expected answer (Redundancy), requirements on the understanding of words' semantic fields (Lexical Entailment) and the use of Synonyms and Paraphrases with respect to the question wording  Furthermore we annotate cases where supporting facts contain Abbreviations of concepts introduced in the question (and vice versa) and when a Dative case substitutes the use of a preposition (e g  “I bought her a gift” vs “I bought a gift for her”)  Regarding syntax, we annotate changes from passive to active Voice, the substitution of a Genitive case with a preposition (e g  “of”) and changes from nominal to verbal style and vice versa (Nominalisation) 
We recognise features that add ambiguity to the supporting facts, for example when information is only expressed implicitly by using an Ellipsis  As opposed to redundant words, we annotate Restrictivity and Factivity modifiers, words and phrases whose presence does change the meaning of a sentence with regard to the expected answer, and occurrences of intra- or inter-sentence Coreference in supporting facts (that is relevant to the question)  Lastly, we mark ambiguous syntactic features, when their resolution is required in order to obtain the answer  Concretely, we mark argument collection with con- and disjunctions (Listing) and ambiguous Prepositions, Coordination Scope and Relative clauses/Adverbial phrases/Appositions 
Framework for MRC Gold Standard Analysis ::: Dimensions of Interest ::: Complexity
Finally, we want to approximate the presence of lexical cues that might simplify the reading required in order to arrive at the answer  Quantifying this allows for more reliable statements about and comparison of the complexity of gold standards, particularly regarding the evaluation of comprehension that goes beyond simple lexical matching  We propose the use of coarse metrics based on lexical overlap between question and context sentences  Intuitively, we aim to quantify how much supporting facts “stand out” from their surrounding passage context  This can be used as proxy for the capability to retrieve the answer BIBREF10  Specifically, we measure (i) the number of words jointly occurring in a question and a sentence, (ii) the length of the longest n-gram shared by question and sentence and (iii) whether a word or n-gram from the question uniquely appears in a sentence 
The resulting taxonomy of the framework is shown in Figure FIGREF10  The full catalogue of features, their description, detailed annotation guideline as well as illustrating examples can be found in Appendix  
Application of the Framework ::: Candidate Datasets
We select contemporary MRC benchmarks to represent all four commonly used problem definitions BIBREF15

ground_truth: 8,275 sentences and 167,739 words in total

The corpus comprises 8,275 sentences and 167,739 words in total.

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 was their highest MRR score?
Context 3: Introduction
BioASQ is a biomedical document classification, document retrieval, and question answering competition, currently in its seventh year  We provide an overview of our submissions to semantic question answering task (7b, Phase B) of BioASQ 7 (except for 'ideal answer' test, in which we did not participate this year)  In this task systems are provided with biomedical questions and are required to submit ideal and exact answers to those questions  We have used BioBERT BIBREF0 based system , see also Bidirectional Encoder Representations from Transformers(BERT) BIBREF1, and we fine tuned it for the biomedical question answering task  Our system scored near the top for factoid questions for all the batches of the challenge  More specifially, in the third test batch set, our system achieved highest ‘MRR’ score for Factoid Question Answering task  Also, for List-type question answering task our system achieved highest recall score in the fourth test batch set  Along with our detailed approach, we present the results for our submissions and also highlight identified downsides for our current approach and ways to improve them in our future experiments  In last test batch results we placed 4th for List-type questions and 3rd for Factoid-type questions )
The QA task is organized in two phases  Phase A deals with retrieval of the relevant document, snippets, concepts, and RDF triples, and phase B deals with exact and ideal answer generations (which is a paragraph size summary of snippets)  Exact answer generation is required for factoid, list, and yes/no type question 
BioASQ organizers provide the training and testing data  The training data consists of questions, gold standard documents, snippets, concepts, and ideal answers (which we did not use in this paper, but we used last year BIBREF2)  The test data is split between phases A and B  The Phase A dataset consists of the questions, unique ids, question types  The Phase B dataset consists of the questions, golden standard documents, snippets, unique ids and question types  Exact answers for factoid type questions are evaluated using strict accuracy (the top answer), lenient accuracy (the top 5 answers), and MRR (Mean Reciprocal Rank) which takes into account the ranks of returned answers  Answers for the list type question are evaluated using precision, recall, and F-measure 
Related Work ::: BioAsq
Sharma et al  BIBREF3 describe a system with two stage process for factoid and list type question answering  Their system extracts relevant entities and then runs supervised classifier to rank the entities  Wiese et al  BIBREF4 propose neural network based model for Factoid and List-type question answering task  The model is based on Fast QA and predicts the answer span in the passage for a given question  The model is trained on SQuAD data set and fine tuned on the BioASQ data  Dimitriadis et al  BIBREF5 proposed two stage process for Factoid question answering task  Their system uses general purpose tools such as Metamap, BeCas to identify candidate sentences  These candidate sentences are represented in the form of features, and are then ranked by the binary classifier  Classifier is trained on candidate sentences extracted from relevant questions, snippets and correct answers from BioASQ challenge  For factoid question answering task highest ‘MRR’ achieved in the 6th edition of BioASQ competition is ‘0 4325’  Our system is a neural network model based on contextual word embeddings BIBREF1 and achieved a ‘MRR’ score ‘0 6103’ in one of the test batches for Factoid Question Answering task 
Related Work ::: A minimum background on BERT
BERT stands for "Bidirectional Encoder Representations from Transformers" BIBREF1 is a contextual word embedding model  Given a sentence as an input, contextual embedding for the words are returned  The BERT model was designed so it can be fine tuned for 11 different tasks BIBREF1, including question answering tasks  For a question answering task, question and paragraph (context) are given as an input  A BERT standard is that question text and paragraph text are separated by a separator [Sep]  BERT question-answering fine tuning involves adding softmax layer  Softmax layer takes contextual word embeddings from BERT as input and learns to identity answer span present in the paragraph (context)  This process is represented in Figure FIGREF4 
BERT was originally trained to perform tasks such as language model creation using masked words and next-sentence-prediction  In other words BERT weights are learned such that context is used in building the representation of the word, not just as a loss function to help learn a context-independent representation  For detailed understanding of BERT Architecture, please refer to the original BERT paper BIBREF1 
Related Work ::: A minimum background on BERT ::: Comparison of Word Embeddings and Contextual Word Embeddings
A ‘word embedding’ is a learned representation  It is represented in the form of vector where words that have the same meaning have a similar vector representation  Consider a word embedding model 'word2vec' BIBREF6 trained on a corpus  Word embeddings generated from the model are context independent that is, word embeddings are returned regardless of where the words appear in a sentence and regardless of e g  the sentiment of the sentence  However, contextual word embedding models like BERT also takes context of the word into consideration 
Related Work ::: Comparison of BERT and Bio-BERT
‘BERT’ and BioBERT are very similar in terms of architecture  Difference is that ‘BERT’ is pretrained on Wikipedia articles, whereas BioBERT version used in our experiments is pretrained on Wikipedia, PMC and PubMed articles  Therefore BioBERT model is expected to perform well with biomedical text, in terms of generating contextual word embeddings 
BioBERT model used in our experiments is based on BERT-Base Architecture; BERT-Base has 12 transformer Layers where as BERT-Large has 24 transformer layers  Moreover contextual word embedding vector size is 768 for BERT-Base and more for BERT-large  According to BIBREF1 Bert-Large, fine-tuned on SQuAD 1 1 question answering data BIBREF7 can achieve F1 Score of 90 9 for Question Answering task where as BERT-Base Fine-tuned on the same SQuAD question answering BIBREF7 data could achieve F1 score of 88 5  One downside of the current version BioBERT is that word-piece vocabulary is the same as that of original BERT Model, as a result word-piece vocabulary does not include biomedical jargon  Lee et al  BIBREF0 created BioBERT, using the same pre-trained BERT released by Google, and hence in the word-piece vocabulary (vocab txt), as a result biomedical jargon is not included in word-piece vocabulary  Modifying word-piece vocabulary (vocab txt) at this stage would loose original compatibility with ‘BERT’, hence it is left unmodified 
In our future work we would like to build pre-trained ‘BERT’ model from scratch  We would pretrain the model with biomedical corpus (PubMed, ‘PMC’) and Wikipedia  Doing so would give us scope to create word piece vocabulary to include biomedical jargon and there are chances of model performing better with biomedical jargon being included in the word piece vocabulary  We will consider this scenario in the future, or wait for the next version of BioBERT 
Experiments: Factoid Question Answering Task
For Factoid Question Answering task, we fine tuned BioBERT BIBREF0 with question answering data and added new features  Fig  FIGREF4 shows the architecture of BioBERT fine tuned for question answering tasks: Input to BioBERT is word tokenized embeddings for question and the paragraph (Context)  As per the ‘BERT’ BIBREF1 standards, tokens ‘[CLS]’ and ‘[SEP]’ are appended to the tokenized input as illustrated in the figure  The resulting model has a softmax layer formed for predicting answer span indices in the given paragraph (Context)  On test data, the fine tuned model generates $n$-best predictions for each question  For a question, $n$-best corresponds that $n$ answers are returned as possible answers in the decreasing order of confidence  Variable $n$ is configurable  In our paper, any further mentions of ‘answer returned by the model’ correspond to the top answer returned by the model 
Experiments: Factoid Question Answering Task ::: Setup
BioASQ provides the training data  This data is based on previous BioASQ competitions  Train data we have considered is aggregate of all train data sets till the 5th version of BioASQ competition  We cleaned the data, that is, question-answering data without answers are removed and left with a total count of ‘530’ question answers  The data is split into train and test data in the ratio of 94 to 6; that is, count of '495' for training and '35' for testing 
The original data format is converted to the BERT/BioBERT format, where BioBERT expects ‘start_index’ of the actual answer  The ‘start_index corresponds to the index of the answer text present in the paragraph/ Context  For finding ‘start_index’ we used built-in python function find()  The function returns the lowest index of the actual answer present in the context(paragraph)  If the answer is not found ‘-1’ is returned as the index  The efficient way of finding start_index is, if the paragraph (Context) has multiple instances of answer text, then ‘start_index’ of the answer should be that instance of answer text whose context actually matches with what’s been asked in the question 
Example (Question, Answer and Paragraph from BIBREF8):
Question: Which drug should be used as an antidote in benzodiazepine overdose?
Answer: 'Flumazenil'
Paragraph(context):
"Flumazenil use in benzodiazepine overdose in the UK: a retrospective survey of NPIS data  OBJECTIVE: Benzodiazepine (BZD) overdose (OD) continues to cause significant morbidity and mortality in the UK  Flumazenil is an effective antidote but there is a risk of seizures, particularly in those who have co-ingested tricyclic antidepressants  A study was undertaken to examine the frequency of use, safety and efficacy of flumazenil in the management of BZD OD in the UK  METHODS: A 2-year retrospective cohort study was performed of all enquiries to the UK National Poisons Information Service involving BZD OD  RESULTS: Flumazenil was administered to 80 patients in 4504 BZD-related enquiries, 68 of whom did not have ventilatory failure or had recognised contraindications to flumazenil  Factors associated with flumazenil use were increased age, severe poisoning and ventilatory failure  Co-ingestion of tricyclic antidepressants and chronic obstructive pulmonary disease did not influence flumazenil administration  Seizure frequency in patients not treated with flumazenil was 0 3%" 
Actual answer is 'Flumazenil', but there are multiple instances of word 'Flu-mazenil'  Efficient way to identify the start-index for 'Flumazenil'(answer) is to find that particular instance of the word 'Flumazenil' which matches the context for the question  In the above example 'Flumazenil' highlighted in bold is the actual instance that matches question's context  Unfortunately, we could not identify readily available tools that can achieve this goal  In our future work, we look forward to handling these scenarios effectively 
Note: The creators of 'SQuAD' BIBREF7 have handled the task of identifying answer's start_index effectively  But 'SQuAD' data set is much more general and does not include biomedical question answering data 
Experiments: Factoid Question Answering Task ::: Training and error analysis
During our training with the BioASQ data, learning rate is set to 3e-5, as mentioned in the BioBERT paper BIBREF0  We started training the model with 495 available train data and 35 test data by setting number of epochs to 50  After training with these hyper-parameters training accuracy(exact match) was 99 3%(overfitting) and testing accuracy is only 4%  In the next iteration we reduced the number of epochs to 25 then training accuracy is reduced to 98 5% and test accuracy moved to 5%  We further reduced number of epochs to 15, and the resulting training accuracy was 70% and test accuracy 15%  In the next iteration set number of epochs to 12 and achieved train accuracy of 57 7% and test accuracy 23 3%  Repeated the experiment with 11 epochs and found training accuracy to be 57 7% and test accuracy to be same 22%  In the next iteration we set number of epochs to '9' and found training accuracy of 48% and test accuracy of 15%  Hence optimum number of epochs is taken as 12 epochs 
During our error analysis we found that on test data, model tends to return text in the beginning of the context(paragraph) as the answer  On analysing train data, we found that there are '120'(out of '495') question answering data instances having start_index:0, meaning 120( 25%) question answering data has first word(s) in the context(paragraph) as the answer  We removed 70% of those instances in order to make train data more balanced  In the new train data set we are left with '411' question answering data instances  This time we got the highest test accuracy of 26% at 11 epochs  We have submitted our results for BioASQ test batch-2, got strict accuracy of 32% and our system stood in 2nd place  Initially, hyper-parameter- 'batch size' is set to ‘400’  Later it is tuned to '32'  Although accuracy(exact answer match) remained at 26%, model generated concise and better answers at batch size ‘32’, that is wrong answers are close to the expected answer in good number of cases 
Example (from BIBREF8)
Question: Which mutated gene causes Chediak Higashi Syndrome?
Exact Answer: ‘lysosomal trafficking regulator gene’ 
The answer returned by a model trained at ‘400’ batch size is ‘Autosomal-recessive complicated spastic paraplegia with a novel lysosomal trafficking regulator’, and from the one trained at ‘32’ batch size is ‘lysosomal trafficking regulator’ 
In further experiments, we have fine tuned the BioBERT model with both ‘SQuAD’ dataset (version 2 0) and BioAsq train data  For training on ‘SQuAD’, hyper parameters- Learning rate and number of epochs are set to ‘3e-3’ and ‘3’ respectively as mentioned in the paper BIBREF1  Test accuracy of the model boosted to 44%  In one more experiment we trained model only on ‘SQuAD’ dataset, this time test accuracy of the model moved to 47%  The reason model did not perform up to the mark when trained with ‘SQuAD’ alongside BioASQ data could be that in formatted BioASQ data, start_index for the answer is not accurate, and affected the overall accuracy 
Our Systems and Their Performance on Factoid Questions
We have experimented with several systems and their variations, e g  created by training with specific additional features (see next subsection)  Here is their list and short descriptions  Unfortunately we did not pay attention to naming, and the systems evolved between test batches, so the overall picture can only be understood by looking at the details 
When we started the experiments our objective was to see whether BioBERT and entailment-based techniques can provide value for in the context of biomedical question answering  The answer to both questions was a yes, qualified by many examples clearly showing the limitations of both methods  Therefore we tried to address some of these limitations using feature engineering with mixed results: some clear errors got corrected and new errors got introduced, without overall improvement but convincing us that in future experiments it might be worth trying feature engineering again especially if more training data were available 
Overall we experimented with several approaches with the following aspects of the systems changing between batches, that is being absent or present:
training on BioAsq data vs  training on SQuAD
using the BioAsq snippets for context vs  using the documents from the provided URLs for context
adding or not the LAT, i e  lexical answer type, feature (see BIBREF9, BIBREF10 and an explanation in the subsection just below) 
For Yes/No questions (only) we experimented with the entailment methods 
We will discuss the performance of these models below and in Section 6  But before we do that, let us discuss a feature engineering experiment which eventually produced mixed results, but where we feel it is potentially useful in future experiments 
Our Systems and Their Performance on Factoid Questions ::: LAT Feature considered and its impact (slightly negative)
During error analysis we found that for some cases, answer being returned by the model is far away from what it is being asked in the Question 
Example: (from BIBREF8)
Question: Hy's law measures failure of which organ?
Actual Answer: ‘Liver’ 
The answer returned by one of our models was ‘alanine aminotransferase’, which is an enzyme  The model returns an enzyme, when the question asked for the organ name  To address this type of errors, we decided to try the concepts of ‘Lexical Answer Type’ (LAT) and Focus Word, which was used in IBM Watson, see BIBREF11 for overview; BIBREF10 for technical details, and BIBREF9 for details on question analysis  In an example given in the last source we read:
POETS & POETRY: He was a bank clerk in the Yukon before he published "Songs of a Sourdough" in 1907 
The focus is the part of the question that is a reference to the answer  In the example above, the focus is "he" 
LATs are terms in the question that indicate what type of entity is being asked for 
The headword of the focus is generally a LAT, but questions often contain additional LATs, and in the Jeopardy! domain, categories are an additional source of LATs 
(   ) In the example, LATs are "he", "clerk", and "poet" 
For example in the question "Which plant does oleuropein originate from?" (BIBREF8)  The LAT here is ‘plant’  For the BioAsq task we did not need to explicitly distinguish between the focus and the LAT concepts  In this example, the expectation is that answer returned by the model is a plant  Thus it is conceivable that the cosine distance between contextual embedding of word 'plant' in the question and contextual embedding for the answer present in the paragraph(context) is comparatively low  As a result model learns to adjust its weights during training phase and returns answers with low cosine distance with the LAT 
We used Stanford CoreNLP BIBREF12 library to write rules for extracting lexical answer type present in the question, both 'parts of speech'(POS) and dependency parsing functionality was used  We incorporated the Lexical Answer Type into one of our systems, UNCC_QA1 in Batch 4  This system underperformed our system FACTOIDS by about 3% in the MRR measure, but corrected errors such as in the example above 
Our Systems and Their Performance on Factoid Questions ::: LAT Feature considered and its impact (slightly negative) ::: Assumptions and rules for deriving lexical answer type 
There are different question types: ‘Which’, ‘What’, ‘When’, ‘How’ etc  Each type of question is being handled differently and there are commonalities among the rules written for different question types  Question words are identified through parts of speech tags: 'WDT', 'WRB' ,'WP'  We assumed that LAT is a ‘Noun’ and follows the question word  Often it was also a subject (nsubj)  This process is illustrated in Fig FIGREF15 
LAT computation was governed by a few simple rules, e g  when a question has multiple words that are 'Subjects’ (and ‘Noun’), a word that is in proximity to the question word is considered as ‘LAT’  These rules are different for each "Wh" word 
Namely, when the word immediately following the question word is a Noun, window size is set to ‘3’  The window size ‘3’ means we iterate through the next ‘3’ words to check if any of the word is both Noun and Subject, If so, such word is considered the ‘LAT’; else the word that is present very next to the question word is considered as the ‘LAT’ 
For questions with words ‘Which’ , ‘What’, ‘When’; a Noun immediately following the question word is very often the LAT, e g  'enzyme' in Which enzyme is targeted by Evolocumab?  When the word immediately following the question word is not a Noun, e g  in What is the function of the protein Magt1? the window size is set to ‘5’, and we iterate through the next ‘5’ words (if present) and search for the word that is both Noun and Subject  If present, the word is considered as the ‘LAT’; else, the Noun in close proximity to the question word and following it is returned as the ‘LAT’ 
For questions with question words: ‘When’, ‘Who’, ‘Why’, the ’LAT’ is a question word itself  For the word ‘How', e g  in How many selenoproteins are encoded in the human genome?, we look at the adjective and if we find one, we take it to be the LAT, otherwise the word 'How' is considered as the ‘LAT’ 
Perhaps because of using only very simple rules, the accuracy for ‘LAT’ derivation is 75%; that is, in the remaining 25% of the cases the LAT word is identified incorrectly  Worth noting is that the overall performance the system that used LATs was slightly inferior to the system without LATs, but the types of errors changed  The training used BioBERT with the LAT feature as part of the input string  The errors it introduces usually involve finding the wrong element of the correct type e g  wrong enzyme when two similar enzymes are described in the text, or 'neuron' when asked about a type of cell with a certain function, when the answer calls for a different cell category, adipocytes, and both are mentioned in the text  We feel with more data and additional tuning or perhaps using an ensemble model, we might be able to keep the correct answers, and improve the results on the confusing examples like the one mentioned above  Therefore if we improve our ‘LAT’ derivation logic, or have larger datasets, then perhaps the neural network techniques they will yield better results 
Our Systems and Their Performance on Factoid Questions ::: Impact of Training using BioAsq data (slightly negative)
Training on BioAsq data in our entry in Batch 1 and Batch 2 under the name QA1 showed it might lead to overfitting  This happened both with (Batch 2) and without (Batch 1) hyperparameters tuning: abysmal 18% MRR in Batch 1, and slighly better one, 40% in Batch 2 (although in Batch 2 it was overall the second best result in MRR but 16% lower than the highest score) 
In Batch 3 (only), our UNCC_QA3 system was fine tuned on BioAsq and SQuAD 2 0 BIBREF7, and for data preprocessing Context paragraph is generated from relevant snippets provided in the test data  This system underperformed, by about 2% in MRR, our other entry UNCC_QA1, which was also an overall category winner for this batch  The latter was also trained on SQuAD, but not on BioAsq  We suspect that the reason could be the simplistic nature of the find() function described in Section 3 1  So, this could be an area where a better algorithm for finding the best occurrence of an entity could improve performance 
Our Systems and Their Performance on Factoid Questions ::: Impact of Using Context from URLs (negative)
In some experiments, for context in testing, we used documents for which URL pointers are provided in BioAsq  However, our system UNCC_QA3 underperformed our other system tested only on the provided snippets 
In Batch 5 the underperformance was about 6% of MRR, compared to our best system UNCC_QA1, and by 9% to the top performer 
Performance on Yes/No and List questions
Our work focused on Factoid questions  But we also have done experiments on List-type and Yes/No questions 
Performance on Yes/No and List questions ::: Entailment improves Yes/No accuracy
We started by answering always YES (in batch 2 and 3) to get the baseline performance  For batch 4 we used entailment  Our algorithm was very simple: Given a question we iterate through the candidate sentences and try to find any candidate sentence is contradicting the question (with confidence over 50%), if so 'No' is returned as answer, else 'Yes' is returned  In batch 4 this strategy produced better than the BioAsq baseline performance, and compared to our other systems, the use of entailment increased the performance by about 13% (macro F1 score)  We used 'AllenNlp' BIBREF13 entailment library to find entailment of the candidate sentences with question 
Performance on Yes/No and List questions ::: For List-type the URLs have negative impact
Overall, we followed the similar strategy that's been followed for Factoid Question Answering task  We started our experiment with batch 2, where we submitted 20 best answers (with context from snippets)  Starting with batch 3, we performed post processing: once models generate answer predictions (n-best predictions), we do post-processing on the predicted answers  In test batch 4, our system (called FACTOIDS) achieved highest recall score of ‘0 7033’ but low precision of 0 1119, leaving open the question of how could we have better balanced the two measures 
In the post-processing phase, we take the top ‘20’ (batch 3) and top 5 (batch 4 and 5), predicted answers, tokenize them using common separators: 'comma' , 'and', 'also', 'as well as'  Tokens with characters count more than ‘100’ are eliminated and rest of the tokens are added to the list of possible answers  BioASQ evaluation mechanism does not consider snippets with more than ‘100’ characters as a valid answer  Considering lengthy snippets in to the list of answers would reduce the mean precision score  As a final step, duplicate snippets in the answer pool are removed  For example, consider these top 3 answers predicted by the system (before post-processing):
{
"text": "dendritic cells",
"probability": 0 7554540733426441,
"start_logit": 8 466046333312988,
"end_logit": 9 536355018615723
},
{
"text": "neutrophils, macrophages and
distinct subtypes of dendritic cells",
"probability": 0 13806867348304214,
"start_logit": 6 766478538513184,
"end_logit": 9 536355018615723
},
{
"text": "macrophages and distinct subtypes of dendritic",
"probability": 0 013973475271178242,
"start_logit": 6 766478538513184,
"end_logit": 7 24576473236084
},
After execution of post-processing heuristics, the list of answers returned is as follows:
["dendritic cells"],
["neutrophils"],
["macrophages"],
["distinct subtypes of dendritic cells"]
Summary of our results
The tables below summarize all our results  They show that the performance of our systems was mixed  The simple architectures and algorithm we used worked very well only in Batch 3  However, we feel we can built a better system based on this experience  In particular we observed both the value of contextual embeddings and of feature engineering (LAT), however we failed to combine them properly 
Summary of our results ::: Factoid questions ::: Systems used in Batch 5 experiments
System description for ‘UNCC_QA1’: The system was finetuned on the SQuAD 2 0  For data preprocessing Context / paragraph was generated from relevant snippets provided in the test data 
System description for ‘QA1’ : ‘LAT’ feature was added and finetuned with SQuAD 2 0  For data preprocessing Context / paragraph was generated from relevant snippets provided in the test data 
System description for ‘UNCC_QA3’ : Fine tuning process is same as it is done for the system ‘UNCC_QA1’ in test batch-5  Difference is during data preprocessing, Context/paragraph is generated from the relevant documents for which URLS are included in the test data 
Summary of our results ::: List Questions
For List-type questions, although post processing helped in the later batches, we never managed to obtain competitive precision, although our recall was good 
Summary of our results ::: Yes/No questions
The only thing worth remembering from our performance is that using entailment can have a measurable impact (at least with respect to a weak baseline)  The results (weak) are in Table 3 
Discussion, Future Experiments, and Conclusions ::: Summary:
In contrast to 2018, when we submitted BIBREF2 to BioASQ a system based on extractive summarization (and scored very high in the ideal answer category), this year we mainly targeted factoid question answering task and focused on experimenting with BioBERT  After these experiments we see the promise of BioBERT in QA tasks, but we also see its limitations  The latter we tried to address with mixed results using feature engineering  Overall these experiments allowed us to secure a best and a second best score in different test batches  Along with Factoid-type question, we also tried ‘Yes/No’ and ‘List’-type questions, and did reasonably well with our very simple approach 
For Yes/No the moral worth remembering is that reasoning has a potential to influence results, as evidenced by our adding the AllenNLP entailment BIBREF13 system increased its performance 
All our data and software is available at Github, in the previously referenced URL (end of Section 2) 
Discussion, Future Experiments, and Conclusions ::: Future experiments
In the current model, we have a shallow neural network with a softmax layer for predicting answer span  Shallow networks however are not good at generalizations  In our future experiments we would like to create dense question answering neural network with a softmax layer for predicting answer span  The main idea is to get contextual word embedding for the words present in the question and paragraph (Context) and feed the contextual word embeddings retrieved from the last layer of BioBERT to the dense question answering network  The mentioned dense layered question answering neural network need to be tuned for finding right hyper parameters  An example of such architecture is shown in Fig FIGREF30 
In one more experiment, we would like to add a better version of ‘LAT’ contextual word embedding as a feature, along with the actual contextual word embeddings for question text, and Context and feed them as input to the dense question answering neural network  By this experiment, we would like to find if ‘LAT’ feature is improving overall answer prediction accuracy  Adding ‘LAT’ feature this way instead of feeding this word piece embedding directly to the BioBERT (as we did in our above experiments) would not downgrade the quality of contextual word embeddings generated form ‘BioBERT'  Quality contextual word embeddings would lead to efficient transfer learning and chances are that it would improve the model's answer prediction accuracy 
We also see potential for incorporating domain specific inference into the task e g  using the MedNLI dataset BIBREF14  For all types of experiments it might be worth exploring clinical BERT embeddings BIBREF15, explicitly incorporating domain knowledge (e g  BIBREF16) and possibly deeper discourse representations (e g  BIBREF17) 
APPENDIX
In this appendix we provide additional details about the implementations 
APPENDIX ::: Systems and their descriptions:
We used several variants of our systems when experimenting with the BioASQ problems  In retrospect, it would be much easier to understand the changes if we adopted some mnemonic conventions in naming the systems  So, we apologize for the names that do not reflect the modifications, and necessitate this list 
APPENDIX ::: Systems and their descriptions: ::: Factoid Type Question Answering:
We preprocessed the test data to convert test data to BioBERT format, We generated Context/paragraph by either aggregating relevant snippets provided or by aggregating documents for which URLS are provided in the BioASQ test data 
APPENDIX ::: Systems and their descriptions: ::: System description for QA1:
We generated Context/paragraph by aggregating relevant snippets available in the test data and mapped it against the question text and question id  We ignored the content present in the documents (document URLS were provided in the original test data)  The model is finetuned with BioASQ data 
data preprocessing is done in the same way as it is done for test batch-1  Model fine tuned on BioASQ data 
‘LAT’/ Focus word feature added and fine tuned with SQuAD 2 0 [reference]  For data preprocessing Context / paragraph is generated from relevant snippets provided in the test data 
APPENDIX ::: Systems and their descriptions: ::: System description for UNCC_QA_1:
System is finetuned on the SQuAD 2 0 [reference]  For data preprocessing Context / paragraph is generated from relevant snippets provided in the test data 
‘LAT’/ Focus word feature added and fine tuned with SQuAD 2 0 [reference]  For data preprocessing Context / paragraph is generated from relevant snippets provided in the test data 
The System is finetuned on the SQuAD 2 0  For data preprocessing Context / paragraph is generated from relevant snippets provided in the test data 
APPENDIX ::: Systems and their descriptions: ::: System description for UNCC_QA3:
System is finetuned on the SQuAD 2 0 [reference] and BioASQ dataset[] For data preprocessing Context / paragraph is generated from relevant snippets provided in the test data 
Fine tuning process is same as it is done for the system ‘UNCC_QA_1’ in test batch-5  Difference is during data preprocessing, Context/paragraph is generated form from the relevant documents for which URLS are included in the test data 
APPENDIX ::: Systems and their descriptions: ::: System description for UNCC_QA2:
Fine tuning process is same as for ‘UNCC_QA_1 ’  Difference is Context/paragraph is generated form from the relevant documents for which URLS are included in the test data  System ‘UNCC_QA_1’ got the highest ‘MRR’ score in the 3rd test batch set 
APPENDIX ::: Systems and their descriptions: ::: System description for FACTOIDS:
The System is finetuned on the SQuAD 2 0  For data preprocessing Context / paragraph is generated from relevant snippets provided in the test data 
APPENDIX ::: Systems and their descriptions: ::: List Type Questions:
We attempted List type questions starting from test batch ‘2’  Used similar approach that's been followed for Factoid Question answering task  For all the test batch sets, in the data pre processing phase Context/ paragraph is generated either by aggregating relevant snippets or by aggregating documents(URLS) provided in the BioASQ test data 
For test batch-2, model (System: QA1) is finetuned on BioASQ data and submitted top ‘20’ answers predicted by the model as the list of answers  system ‘QA1’ achieved low F-Measure score:‘0 0786’ in the second test batch  In the further test batches for List type questions, we finetuned the model on Squad data set [reference], implemented post processing techniques (refer section 5 2) and achieved a better F-measure score: ‘0 2862’ in the final test batch set 
In test batch-3 (Systems : ‘QA1’/’’UNCC_QA_1’/’UNCC_QA3’/’UNCC_QA2’) top 20 answers returned by the model is sent for post processing and in test batch 4 and 5 only top 5 answers are sent for post processing  System UNCC_QA2(in batch 3) for List type question answering, Context is generated from documents for which URLS are provided in the BioASQ test data  for the rest of the systems (in test batch-3) for List Type question answering task snippets present in the BioaSQ test data are used to generate context 
In test batch-4 (System : ‘FACTOIDS’/’UNCC_QA_1’/’UNCC_QA3’’) top 5 answers returned by the model is sent for post processing  In case of system ‘FACTOIDS’ snippets in the test data were used to generate context  for systems ’UNCC_QA_1’ and ’UNCC_QA3’ context is generated from the documents for which URLS are provided in the BioASQ test data 
In test batch-5 ( Systems: ‘QA1’/’UNCC_QA_1’/’UNCC_QA3’/’UNCC_QA2’ ) our approach is the same as that of test batch-4 where top 5 answers returned by the model is sent for post processing  for all the systems (in test batch-5) context is generated from the snippets provided in the BioASQ test data 
APPENDIX ::: Systems and their descriptions: ::: Yes/No Type Questions:
For the first 3 test batches, We have submitted answer ‘Yes’ to all the questions  Later, we employed ‘Sentence Entailment’ techniques(refer section 6 0) for the fourth and fifth test batch sets  Our Systems with ‘Sentence Entailment’ approach (for ‘Yes’/ ‘No’ question answering): ‘UNCC_QA_1’(test batch-4), UNCC_QA3(test batch-5) 
APPENDIX ::: Additional details for Yes/No Type Questions
We used Textual Entailment in Batch 4 and 5 for ‘Yes’/‘No’ question type  The algorithm was very simple: Given a question we iterate through the candidate sentences, and look for any candidate sentences contradicting the question  If we find one 'No' is returned as answer, else 'Yes' is returned  (The confidence for contradiction was set at 50%) We used AllenNLP BIBREF13 entailment library to find entailment of the candidate sentences with question 
Flow Chart for Yes/No Question answer processing is shown in Fig FIGREF51
APPENDIX ::: Assumptions, rules and logic flow for deriving Lexical Answer Types from questions
There are different question types, and we distinguished them based on the question words: ‘Which’, ‘What’, ‘When’, ‘How’ etc  Each type of question is being handled differently and there are commonalities among the rules written for different question types  How are question words identified? question words have parts of speech(POS): 'WDT', 'WRB', 'WP' 
Assumptions:
1) Lexical answer type (‘LAT’) or focus word is of type Noun and follows the question word 
2) The LAT word is a Subject  (This clearly not always true, but we used a very simple method)  Note: ‘StanfordNLP’ dependency parsing tag for identifying subject is 'nsubj' or 'nsubjpass' 
3) When a question has multiple words that are of type Subject (and Noun), a word that is in proximity to the question word is considered as ‘LAT’ 
4) For questions with question words: ‘When’, ‘Who’, ‘Why’, the ’LAT’ is a question word itself that is, ‘When’, ‘Who’, ‘Why’ respectively 
Rules and logic flow to traverse a question: The three cases below describe the logic flow of finding LATs  The figures show the grammatical structures used for this purpose 
APPENDIX ::: Assumptions, rules and logic flow for deriving Lexical Answer Types from questions ::: Case-1:
Question with question word ‘How’ 
For questions with question word 'How', the adjective that follows the question word is considered as ‘LAT’ (need not follow immediately)  If an adjective is absent, word 'How' is considered as ‘LAT’  When there are multiple words that are adjectives, a word in close proximity to the question word and follows it is returned as ‘LAT’  Note: The part of speech tag to identify adjectives is 'JJ'  For Other possible question words like ‘whose’  ‘LAT’/Focus word is question words itself 
Example Question: How many selenoproteins are encoded in the human genome?
APPENDIX ::: Assumptions, rules and logic flow for deriving Lexical Answer Types from questions ::: Case-2:
Questions with question words ‘Which’ , ‘What’ and all other possible question words; a 'Noun' immediately following the question word 
Example Question: Which enzyme is targeted by Evolocumab?
Here, Focus word/LAT is ‘enzyme’ which is both Noun and Subject and immediately follows the question word 
When the word immediately following the question word is a noun, the window size is set to ‘3’  This size ‘3’ means that we iterate through the next ‘3’ words (if present) to check if any of the word is both 'Noun' and 'Subject', If so, the word is considered as ‘LAT’/Focus Word  Else the word that is present very next to the question word is considered as ‘LAT’ 
APPENDIX ::: Assumptions, rules and logic flow for deriving Lexical Answer Types from questions ::: Case-3:
Questions with question words ‘Which’ , ‘What’ and all other possible question words; word immediately following the question word is not a 'Noun' 
Example Question: What is the function of the protein Magt1?
Here, Focus word/LAT is ‘function ’ which is both Noun and Subject and does not immediately follow the question word 
When the very next word following the question word is not a Noun, window size is set to ‘5’  Window size ‘5’ corresponds that we iterate through the next ‘5’ words (if present) and search for the word that is both Noun and Subject  If present, the word is considered as ‘LAT’  Else, the 'Noun' close proximity to the question word and follows it is returned as ‘LAT’ 
Ad we mentioned earlier, the accuracy for ‘LAT’ derivation is 75 percent  But clearly the simple logic described above can be improved, as shown in BIBREF9, BIBREF10  Whether this in turn produces improvements in this particular task is an open question 
APPENDIX ::: Proposing Future Experiments
In the current model, we have a shallow neural network with a softmax layer for predicting answer span  Shallow networks however are not good at generalizations  In our future experiments we would like to create dense question answering neural network with a softmax layer for predicting answer span  The main idea is to get contextual word embedding for the words present in the question and paragraph (Context) and feed the contextual word embeddings retrieved from the last layer of BioBERT to the dense question answering network  The mentioned dense layered question answering Neural network need to be tuned for finding right hyper parameters  An example of such architecture is shown in Fig FIGREF30 
In another experiment we would like to only feed contextual word embeddings for Focus word/ ‘LAT’, paragraph/ Context as input to the question answering neural network  In this experiment we would neglect all embeddings for the question text except that of Focus word/ ‘LAT’  Our assumption and idea for considering focus word and neglecting remaining words in the question is that during training phase it would make more precise for the model to identify the focus of the question and map answers against the question’s focus  To validate our assumption, we would like to take sample question answering data and find the cosine distance between contextual embedding of Focus word and that of the actual answer and verify if the cosine distance is comparatively low in most of the cases 
In one more experiment, we would like to add a better version of ‘LAT’ contextual word embedding as a feature, along with the actual contextual word embeddings for question text, and Context and feed them as input to the dense question answering neural network  By this experiment, we would like to find if ‘LAT’ feature is improving overall answer prediction accuracy  Adding ‘LAT’ feature this way instead of feeding Focus word’s word piece embedding directly (as we did in our above experiments) to the BioBERT would not downgrade the quality of contextual word embeddings generated form ‘BioBERT'  Quality contextual word embeddings would lead to efficient transfer learning and chances are that it would improve the model's answer prediction accuracy 

ground_truth: 0.5115

0.6103