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 is the dataset annotated?
Context 1: Introduction
In recent years, there has been a movement to leverage social medial data to detect, estimate, and track the change in prevalence of disease  For example, eating disorders in Spanish language Twitter tweets BIBREF0 and influenza surveillance BIBREF1   More recently, social media has been leveraged to monitor social risks such as prescription drug and smoking behaviors BIBREF2 , BIBREF3 , BIBREF4 as well as a variety of mental health disorders including suicidal ideation BIBREF5 , attention deficient hyperactivity disorder BIBREF6 and major depressive disorder BIBREF7   In the case of major depressive disorder, recent efforts range from characterizing linguistic phenomena associated with depression BIBREF8 and its subtypes e g , postpartum depression BIBREF5 , to identifying specific depressive symptoms BIBREF9 , BIBREF10 e g , depressed mood  However, more research is needed to better understand the predictive power of supervised machine learning classifiers and the influence of feature groups and feature sets for efficiently classifying depression-related tweets to support mental health monitoring at the population-level BIBREF11  
This paper builds upon related works toward classifying Twitter tweets representing symptoms of major depressive disorder by assessing the contribution of lexical features (e g , unigrams) and emotion (e g , strongly negative) to classification performance, and by applying methods to eliminate low-value features 
METHODS
Specifically, we conducted a feature ablation study to assess the informativeness of each feature group and a feature elimination study to determine the optimal feature sets for classifying Twitter tweets  We leveraged an existing, annotated Twitter dataset that was constructed based on a hierarchical model of depression-related symptoms BIBREF12 , BIBREF13   The dataset contains 9,473 annotations for 9,300 tweets  Each tweet is annotated as no evidence of depression (e g , “Citizens fear an economic depression") or evidence of depression (e g , “depressed over disappointment")  If a tweet is annotated evidence of depression, then it is further annotated with one or more depressive symptoms, for example, depressed mood (e g , “feeling down in the dumps"), disturbed sleep (e g , “another restless night"), or fatigue or loss of energy (e g , “the fatigue is unbearable") BIBREF10   For each class, every annotation (9,473 tweets) is binarized as the positive class e g , depressed mood=1 or negative class e g , not depressed mood=0 
Features
Furthermore, this dataset was encoded with 7 feature groups with associated feature values binarized (i e , present=1 or absent=0) to represent potentially informative features for classifying depression-related classes  We describe the feature groups by type, subtype, and provide one or more examples of words representing the feature subtype from a tweet:
lexical features, unigrams, e g , “depressed”;
syntactic features, parts of speech, e g , “cried” encoded as V for verb;
emotion features, emoticons, e g , :( encoded as SAD;
demographic features, age and gender e g , “this semester” encoded as an indicator of 19-22 years of age and “my girlfriend” encoded as an indicator of male gender, respectively;
sentiment features, polarity and subjectivity terms with strengths, e g , “terrible” encoded as strongly negative and strongly subjective;
personality traits, neuroticism e g , “pissed off” implies neuroticism;
LIWC Features, indicators of an individual's thoughts, feelings, personality, and motivations, e g , “feeling” suggestions perception, feeling, insight, and cognitive mechanisms experienced by the Twitter user 
A more detailed description of leveraged features and their values, including LIWC categories, can be found in BIBREF10  
Based on our prior initial experiments using these feature groups BIBREF10 , we learned that support vector machines perform with the highest F1-score compared to other supervised approaches  For this study, we aim to build upon this work by conducting two experiments: 1) to assess the contribution of each feature group and 2) to determine the optimal percentile of top ranked features for classifying Twitter tweets in the depression schema hierarchy 
Feature Contribution
Feature ablation studies are conducted to assess the informativeness of a feature group by quantifying the change in predictive power when comparing the performance of a classifier trained with the all feature groups versus the performance without a particular feature group  We conducted a feature ablation study by holding out (sans) each feature group and training and testing the support vector model using a linear kernel and 5-fold, stratified cross-validation  We report the average F1-score from our baseline approach (all feature groups) and report the point difference (+ or -) in F1-score performance observed by ablating each feature set 
By ablating each feature group from the full dataset, we observed the following count of features - sans lexical: 185, sans syntactic: 16,935, sans emotion: 16,954, sans demographics: 16,946, sans sentiment: 16,950, sans personality: 16,946, and sans LIWC: 16,832  In Figure 1, compared to the baseline performance, significant drops in F1-scores resulted from sans lexical for depressed mood (-35 points), disturbed sleep (-43 points), and depressive symptoms (-45 points)  Less extensive drops also occurred for evidence of depression (-14 points) and fatigue or loss of energy (-3 points)  In contrast, a 3 point gain in F1-score was observed for no evidence of depression  We also observed notable drops in F1-scores for disturbed sleep by ablating demographics (-7 points), emotion (-5 points), and sentiment (-5 points) features  These F1-score drops were accompanied by drops in both recall and precision  We found equal or higher F1-scores by removing non-lexical feature groups for no evidence of depression (0-1 points), evidence of depression (0-1 points), and depressive symptoms (2 points) 
Unsurprisingly, lexical features (unigrams) were the largest contributor to feature counts in the dataset  We observed that lexical features are also critical for identifying depressive symptoms, specifically for depressed mood and for disturbed sleep  For the classes higher in the hierarchy - no evidence of depression, evidence of depression, and depressive symptoms - the classifier produced consistent F1-scores, even slightly above the baseline for depressive symptoms and minor fluctuations of change in recall and precision when removing other feature groups suggesting that the contribution of non-lexical features to classification performance was limited  However, notable changes in F1-score were observed for the classes lower in the hierarchy including disturbed sleep and fatigue or loss of energy  For instance, changes in F1-scores driven by both recall and precision were observed for disturbed sleep by ablating demographics, emotion, and sentiment features, suggesting that age or gender (“mid-semester exams have me restless”), polarity and subjective terms (“lack of sleep is killing me”), and emoticons (“wide awake :(”) could be important for both identifying and correctly classifying a subset of these tweets 
Feature Elimination
Feature elimination strategies are often taken 1) to remove irrelevant or noisy features, 2) to improve classifier performance, and 3) to reduce training and run times  We conducted an experiment to determine whether we could maintain or improve classifier performances by applying the following three-tiered feature elimination approach:
Reduction We reduced the dataset encoded for each class by eliminating features that occur less than twice in the full dataset 
Selection We iteratively applied Chi-Square feature selection on the reduced dataset, selecting the top percentile of highest ranked features in increments of 5 percent to train and test the support vector model using a linear kernel and 5-fold, stratified cross-validation 
Rank We cumulatively plotted the average F1-score performances of each incrementally added percentile of top ranked features  We report the percentile and count of features resulting in the first occurrence of the highest average F1-score for each class 
All experiments were programmed using scikit-learn 0 18 
The initial matrices of almost 17,000 features were reduced by eliminating features that only occurred once in the full dataset, resulting in 5,761 features  We applied Chi-Square feature selection and plotted the top-ranked subset of features for each percentile (at 5 percent intervals cumulatively added) and evaluated their predictive contribution using the support vector machine with linear kernel and stratified, 5-fold cross validation 
In Figure 2, we observed optimal F1-score performance using the following top feature counts: no evidence of depression: F1: 87 (15th percentile, 864 features), evidence of depression: F1: 59 (30th percentile, 1,728 features), depressive symptoms: F1: 55 (15th percentile, 864 features), depressed mood: F1: 39 (55th percentile, 3,168 features), disturbed sleep: F1: 46 (10th percentile, 576 features), and fatigue or loss of energy: F1: 72 (5th percentile, 288 features) (Figure 1)  We note F1-score improvements for depressed mood from F1: 13 at the 1st percentile to F1: 33 at the 20th percentile 
We observed peak F1-score performances at low percentiles for fatigue or loss of energy (5th percentile), disturbed sleep (10th percentile) as well as depressive symptoms and no evidence of depression (both 15th percentile) suggesting fewer features are needed to reach optimal performance  In contrast, peak F1-score performances occurred at moderate percentiles for evidence of depression (30th percentile) and depressed mood (55th percentile) suggesting that more features are needed to reach optimal performance  However, one notable difference between these two classes is the dramatic F1-score improvements for depressed mood i e , 20 point increase from the 1st percentile to the 20th percentile compared to the more gradual F1-score improvements for evidence of depression i e , 11 point increase from the 1st percentile to the 20th percentile  This finding suggests that for identifying depressed mood a variety of features are needed before incremental gains are observed 
RESULTS
From our annotated dataset of Twitter tweets (n=9,300 tweets), we conducted two feature studies to better understand the predictive power of several feature groups for classifying whether or not a tweet contains no evidence of depression (n=6,829 tweets) or evidence of depression (n=2,644 tweets)  If there was evidence of depression, we determined whether the tweet contained one or more depressive symptoms (n=1,656 tweets) and further classified the symptom subtype of depressed mood (n=1,010 tweets), disturbed sleep (n=98 tweets), or fatigue or loss of energy (n=427 tweets) using support vector machines  From our prior work BIBREF10 and in Figure 1, we report the performance for prediction models built by training a support vector machine using 5-fold, stratified cross-validation with all feature groups as a baseline for each class  We observed high performance for no evidence of depression and fatigue or loss of energy and moderate performance for all remaining classes 
Discussion
We conducted two feature study experiments: 1) a feature ablation study to assess the contribution of feature groups and 2) a feature elimination study to determine the optimal percentile of top ranked features for classifying Twitter tweets in the depression schema hierarchy 
Future Work
Our next step is to address the classification of rarer depressive symptoms suggestive of major depressive disorder from our dataset and hierarchy including inappropriate guilt, difficulty concentrating, psychomotor agitation or retardation, weight loss or gain, and anhedonia BIBREF15 , BIBREF16   We are developing a population-level monitoring framework designed to estimate the prevalence of depression (and depression-related symptoms and psycho-social stressors) over millions of United States-geocoded tweets  Identifying the most discriminating feature sets and natural language processing classifiers for each depression symptom is vital for this goal 
Conclusions
In summary, we conducted two feature study experiments to assess the contribution of feature groups and to determine the optimal percentile of top ranked features for classifying Twitter tweets in the depression schema hierarchy  From these experiments, we conclude that simple lexical features and reduced feature sets can produce comparable results to the much larger feature dataset 
Acknowledgments
Research reported in this publication was supported by the National Library of Medicine of the [United States] National Institutes of Health under award numbers K99LM011393 and R00LM011393  This study was granted an exemption from review by the University of Utah Institutional Review Board (IRB 00076188)  Note that in order to protect tweeter anonymity, we have not reproduced tweets verbatim  Example tweets shown were generated by the researchers as exemplars only  Finally, we would like to thank the anonymous reviewers of this paper for their valuable comments 
Context 2: Introduction
The irony is a kind of figurative language, which is widely used on social media BIBREF0   The irony is defined as a clash between the intended meaning of a sentence and its literal meaning BIBREF1   As an important aspect of language, irony plays an essential role in sentiment analysis BIBREF2 , BIBREF0 and opinion mining BIBREF3 , BIBREF4  
Although some previous studies focus on irony detection, little attention is paid to irony generation  As ironies can strengthen sentiments and express stronger emotions, we mainly focus on generating ironic sentences  Given a non-ironic sentence, we implement a neural network to transfer it to an ironic sentence and constrain the sentiment polarity of the two sentences to be the same  For example, the input is “I hate it when my plans get ruined" which is negative in sentiment polarity and the output should be ironic and negative in sentiment as well, such as “I like it when my plans get ruined"  The speaker uses “like" to be ironic and express his or her negative sentiment  At the same time, our model can preserve contents which are irrelevant to sentiment polarity and irony  According to the categories mentioned in BIBREF5 , irony can be classified into 3 classes: verbal irony by means of a polarity contrast, the sentences containing expression whose polarity is inverted between the intended and the literal evaluation; other types of verbal irony, the sentences that show no polarity contrast between the literal and intended meaning but are still ironic; and situational irony, the sentences that describe situations that fail to meet some expectations  As ironies in the latter two categories are obscure and hard to understand, we decide to only focus on ironies in the first category in this work  For example, our work can be specifically described as: given a sentence “I hate to be ignored", we train our model to generate an ironic sentence such as “I love to be ignored"  Although there is “love" in the generated sentence, the speaker still expresses his or her negative sentiment by irony  We also make some explorations in the transformation from ironic sentences to non-ironic sentences at the end of our work  Because of the lack of previous work and baselines on irony generation, we implement our model based on style transfer  Our work will not only provide the first large-scale irony dataset but also make our model as a benchmark for the irony generation 
Recently, unsupervised style transfer becomes a very popular topic  Many state-of-the-art studies try to solve the task with sequence-to-sequence (seq2seq) framework  There are three main ways to build up models  The first is to learn a latent style-independent content representation and generate sentences with the content representation and another style BIBREF6 , BIBREF7   The second is to directly transfer sentences from one style to another under the control of classifiers and reinforcement learning BIBREF8   The third is to remove style attribute words from the input sentence and combine the remaining content with new style attribute words BIBREF9 , BIBREF10   The first method usually obtains better performances via adversarial training with discriminators  The style-independent content representation, nevertheless, is not easily obtained BIBREF11 , which results in poor performances  The second method is suitable for complex styles which are difficult to model and describe  The model can learn the deep semantic features by itself but sometimes the model is sensitive to parameters and hard to train  The third method succeeds to preserve content but cannot work for some complex styles such as democratic and republican  Sentences with those styles usually do not have specific style attribute words  Unfortunately, due to the lack of large irony dataset and difficulties of modeling ironies, there has been little work trying to generate ironies based on seq2seq framework as far as we know  Inspired by methods for style transfer, we decide to implement a specifically designed model based on unsupervised style transfer to explore irony generation 
In this paper, in order to address the lack of irony data, we first crawl over 2M tweets from twitter to build a dataset with 262,755 ironic and 112,330 non-ironic tweets  Then, due to the lack of parallel data, we propose a novel model to transfer non-ironic sentences to ironic sentences in an unsupervised way  As ironic style is hard to model and describe, we implement our model with the control of classifiers and reinforcement learning  Different from other studies in style transfer, the transformation from non-ironic to ironic sentences has to preserve sentiment polarity as mentioned above  Therefore, we not only design an irony reward to control the irony accuracy and implement denoising auto-encoder and back-translation to control content preservation but also design a sentiment reward to control sentiment preservation 
Experimental results demonstrate that our model achieves a high irony accuracy with well-preserved sentiment and content  The contributions of our work are as follows:
Related Work
Style Transfer: As irony is a complicated style and hard to model with some specific style attribute words, we mainly focus on studies without editing style attribute words 
Some studies are trying to disentangle style representation from content representation  In BIBREF12 , authors leverage adversarial networks to learn separate content representations and style representations  In BIBREF13 and BIBREF6 , researchers combine variational auto-encoders (VAEs) with style discriminators 
However, some recent studies BIBREF11 reveal that the disentanglement of content and style representations may not be achieved in practice  Therefore, some other research studies BIBREF9 , BIBREF10 strive to separate content and style by removing stylistic words  Nonetheless, many non-ironic sentences do not have specific stylistic words and as a result, we find it difficult to transfer non-ironic sentences to ironic sentences through this way in practice 
Besides, some other research studies do not disentangle style from content but directly learn representations of sentences  In BIBREF8 , authors propose a dual reinforcement learning framework without separating content and style representations  In BIBREF7 , researchers utilize a machine translation model to learn a sentence representation preserving the meaning of the sentence but reducing stylistic properties  In this method, the quality of generated sentences relies on the performance of classifiers to a large extent  Meanwhile, such models are usually sensitive to parameters and difficult to train  In contrast, we combine a pre-training process with reinforcement learning to build up a stable language model and design special rewards for our task 
Irony Detection: With the development of social media, irony detection becomes a more important task  Methods for irony detection can be mainly divided into two categories: methods based on feature engineering and methods based on neural networks 
As for methods based on feature engineering, In BIBREF1 , authors investigate pragmatic phenomena and various irony markers  In BIBREF14 , researchers leverage a combination of sentiment, distributional semantic and text surface features  Those models rely on hand-crafted features and are hard to implement 
When it comes to methods based on neural networks, long short-term memory (LSTM) BIBREF15 network is widely used and is very efficient for irony detection  In BIBREF16 , a tweet is divided into two segments and a subtract layer is implemented to calculate the difference between two segments in order to determine whether the tweet is ironic  In BIBREF17 , authors utilize a recurrent neural network with Bi-LSTM and self-attention without hand-crafted features  In BIBREF18 , researchers propose a system based on a densely connected LSTM network 
Our Dataset
In this section, we describe how we build our dataset with tweets  First, we crawl over 2M tweets from twitter using GetOldTweets-python  We crawl English tweets from 04/09/2012 to /12/18/2018  We first remove all re-tweets and use langdetect to remove all non-English sentences  Then, we remove hashtags attached at the end of the tweets because they are usually not parts of sentences and will confuse our language model  After that, we utilize Ekphrasis to process tweets  We remove URLs and restore remaining hashtags, elongated words, repeated words, and all-capitalized words  To simplify our dataset, We replace all “ INLINEFORM0 money INLINEFORM1 " and “ INLINEFORM2 time INLINEFORM3 " tokens with “ INLINEFORM4 number INLINEFORM5 " token when using Ekphrasis  And we delete sentences whose lengths are less than 10 or greater than 40  In order to restore abbreviations, we download an abbreviation dictionary from webopedia and restore abbreviations to normal words or phrases according to the dictionary  Finally, we remove sentences which have more than two rare words (appearing less than three times) in order to constrain the size of vocabulary  Finally, we get 662,530 sentences after pre-processing 
As neural networks are proved effective in irony detection, we decide to implement a neural classifier in order to classify the sentences into ironic and non-ironic sentences  However, the only high-quality irony dataset we can obtain is the dataset of Semeval-2018 Task 3 and the dataset is pretty small, which will cause overfitting to complex models  Therefore, we just implement a simple one-layer RNN with LSTM cell to classify pre-processed sentences into ironic sentences and non-ironic sentences because LSTM networks are widely used in irony detection  We train the model with the dataset of Semeval-2018 Task 3  After classification, we get 262,755 ironic sentences and 399,775 non-ironic sentences  According to our observation, not all non-ironic sentences are suitable to be transferred into ironic sentences  For example, “just hanging out   watching   is it monday yet" is hard to transfer because it does not have an explicit sentiment polarity  So we remove all interrogative sentences from the non-ironic sentences and only obtain the sentences which have words expressing strong sentiments  We evaluate the sentiment polarity of each word with TextBlob and we view those words with sentiment scores greater than 0 5 or less than -0 5 as words expressing strong sentiments  Finally, we build our irony dataset with 262,755 ironic sentences and 102,330 non-ironic sentences 
[t] Irony Generation Algorithm
INLINEFORM0 pre-train with auto-encoder Pre-train INLINEFORM1 , INLINEFORM2 with INLINEFORM3 using MLE based on Eq  EQREF16 Pre-train INLINEFORM4 , INLINEFORM5 with INLINEFORM6 using MLE based on Eq  EQREF17 INLINEFORM7 pre-train with back-translation Pre-train INLINEFORM8 , INLINEFORM9 , INLINEFORM10 , INLINEFORM11 with INLINEFORM12 using MLE based on Eq  EQREF19 Pre-train INLINEFORM13 , INLINEFORM14 , INLINEFORM15 , INLINEFORM16 with INLINEFORM17 using MLE based on Eq  EQREF20
INLINEFORM0 train with RL each epoch e = 1, 2,    , INLINEFORM1 INLINEFORM2 train non-irony2irony with RL INLINEFORM3 in N INLINEFORM4 update INLINEFORM5 , INLINEFORM6 , using INLINEFORM7 based on Eq  EQREF29 INLINEFORM8 back-translation INLINEFORM9 INLINEFORM10 INLINEFORM11 update INLINEFORM12 , INLINEFORM13 , INLINEFORM14 , INLINEFORM15 using MLE based on Eq  EQREF19 INLINEFORM16 train irony2non-irony with RL INLINEFORM17 in I INLINEFORM18 update INLINEFORM19 , INLINEFORM20 , using INLINEFORM21 similar to Eq  EQREF29 INLINEFORM22 back-translation INLINEFORM23 INLINEFORM24 INLINEFORM25 update INLINEFORM26 , INLINEFORM27 , INLINEFORM28 , INLINEFORM29 using MLE based on Eq  EQREF20
Our Method
Given two non-parallel corpora: non-ironic corpus N={ INLINEFORM0 , INLINEFORM1 ,    , INLINEFORM2 } and ironic corpus I={ INLINEFORM3 , INLINEFORM4 ,    , INLINEFORM5 }, the goal of our irony generation model is to generate an ironic sentence from a non-ironic sentence while preserving the content and sentiment polarity of the source input sentence  We implement an encoder-decoder framework where two encoders are utilized to encode ironic sentences and non-ironic sentences respectively and two decoders are utilized to decode ironic sentences and non-ironic sentences from latent representations respectively  In order to enforce a shared latent space, we share two layers on both the encoder side and the decoder side  Our model architecture is illustrated in Figure FIGREF13   We denote irony encoder as INLINEFORM6 , irony decoder as INLINEFORM7 and non-irony encoder as INLINEFORM8 , non-irony decoder as INLINEFORM9   Their parameters are INLINEFORM10 , INLINEFORM11 , INLINEFORM12 and INLINEFORM13  
Our irony generation algorithm is shown in Algorithm SECREF3   We first pre-train our model using denoising auto-encoder and back-translation to build up language models for both styles (section SECREF14 )  Then we implement reinforcement learning to train the model to transfer sentences from one style to another (section SECREF21 )  Meanwhile, to achieve content preservation, we utilize back-translation for one time in every INLINEFORM0 time steps 
Pretraining
In order to build up our language model and preserve the content, we apply the auto-encoder model  To prevent the model from simply copying the input sentence, we randomly add some noises in the input sentence
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

ground_truth: no evidence of depression, depressed mood, disturbed sleep, fatigue or loss of energy

The annotations are based on evidence of depression and further annotated by the depressive symptom if there is evidence of depression

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 experiments are conducted?
Context 2:  Specifically, for every word in the input sentence, there is 10% chance that we delete it, 10 % chance that we duplicate it, 10% chance that we swap it with the next word, or it remains unchanged  We first encode the input sentence INLINEFORM0 or INLINEFORM1 with respective encoder INLINEFORM2 or INLINEFORM3 to obtain its latent representation INLINEFORM4 or INLINEFORM5 and reconstruct the input sentence with the latent representation and respective decoder  So we can get the reconstruction loss for auto-encoder INLINEFORM6 : DISPLAYFORM0 DISPLAYFORM1
In addition to denoising auto-encoder, we implement back-translation BIBREF19 to generate a pseudo-parallel corpus  Suppose our model takes non-ironic sentence INLINEFORM0 as input  We first encode INLINEFORM1 with INLINEFORM2 to obtain its latent representation INLINEFORM3 and decode the latent representation with INLINEFORM4 to get a transferred sentence INLINEFORM5   Then we encode INLINEFORM6 with INLINEFORM7 and decode its latent representation with INLINEFORM8 to reconstruct the original input sentence INLINEFORM9   Therefore, our reconstruction loss for back-translation INLINEFORM10 : DISPLAYFORM0
And if our model takes ironic sentence INLINEFORM0 as input, we can get the reconstruction loss for back-translation as: DISPLAYFORM0
Reinforcement Learning
Since the gold transferred result of input is unavailable, we cannot evaluate the quality of the generated sentence directly  Therefore, we implement reinforcement learning and elaborately design two rewards to describe the irony accuracy and sentiment preservation, respectively 
A pre-trained binary irony classifier based on CNN BIBREF20 is used to evaluate how ironic a sentence is  We denote the parameter of the classifier as INLINEFORM0 and it is fixed during the training process 
In order to facilitate the transformation, we design the irony reward as the difference between the irony score of the input sentence and that of the output sentence  Formally, when we input a non-ironic sentence INLINEFORM0 and transfer it to an ironic sentence INLINEFORM1 , our irony reward is defined as: DISPLAYFORM0
where INLINEFORM0 denotes ironic style and INLINEFORM1 is the probability of that a sentence INLINEFORM2 is ironic 
To preserve the sentiment polarity of the input sentence, we also need to use classifiers to evaluate the sentiment polarity of the sentences  However, the sentiment analysis of ironic sentences and non-ironic sentences are different  In the case of figurative languages such as irony, sarcasm or metaphor, the sentiment polarity of the literal meaning may differ significantly from that of the intended figurative meaning BIBREF0   As we aim to train our model to transfer sentences from non-ironic to ironic, using only one classifier is not enough  As a result, we implement two pre-trained sentiment classifiers for non-ironic sentences and ironic sentences respectively  We denote the parameter of the sentiment classifier for ironic sentences as INLINEFORM0 and that of the sentiment classifier for non-ironic sentences as INLINEFORM1  
A challenge, when we implement two classifiers to evaluate the sentiment polarity, is that the two classifiers trained with different datasets may have different distributions of scores  That means we cannot directly calculate the sentiment reward with scores applied by two classifiers  To alleviate this problem and standardize the prediction results of two classifiers, we set a threshold for each classifier and subtract the respective threshold from scores applied by the classifier to obtain the comparative sentiment polarity score  We get the optimal threshold by maximizing the ability of the classifier according to the distribution of our training data 
We denote the threshold of ironic sentiment classifier as INLINEFORM0 and the threshold of non-ironic sentiment classifier as INLINEFORM1   The standardized sentiment score is defined as INLINEFORM2 and INLINEFORM3 where INLINEFORM4 denotes the positive sentiment polarity and INLINEFORM5 is the probability of that a sentence is positive in sentiment polarity 
As mentioned above, the input sentence and the generated sentence should express the same sentiment  For example, if we input a non-ironic sentence “I hate to be ignored" which is negative in sentiment polarity, the generated ironic sentence should be also negative, such as “I love to be ignored"  To achieve sentiment preservation, we design the sentiment reward as that one minus the absolute value of the difference between the standardized sentiment score of the input sentence and that of the generated sentence  Formally, when we input a non-ironic sentence INLINEFORM0 and transfer it to an ironic sentence INLINEFORM1 , our sentiment reward is defined as: DISPLAYFORM0
To encourage our model to focus on both the irony accuracy and the sentiment preservation, we apply the harmonic mean of irony reward and sentiment reward: DISPLAYFORM0
Policy Gradient
The policy gradient algorithm BIBREF21 is a simple but widely-used algorithm in reinforcement learning  It is used to maximize the expected reward INLINEFORM0   The objective function to minimize is defined as: DISPLAYFORM0
where INLINEFORM0 , INLINEFORM1 is the reward of INLINEFORM2 and INLINEFORM3 is the input size 
Training Details
INLINEFORM0 , INLINEFORM1 , INLINEFORM2 and INLINEFORM3 in our model are Transformers BIBREF22 with 4 layers and 2 shared layers  The word embeddings of 128 dimensions are learned during the training process  Our maximum sentence length is set as 40  The optimizer is Adam BIBREF23 and the learning rate is INLINEFORM4   The batch size is 32 and harmonic weight INLINEFORM5 in Eq 9 is 0 5  We set the interval INLINEFORM6 as 200  The model is pre-trained for 6 epochs and trained for 15 epochs for reinforcement learning 
Irony Classifier: We implement a CNN classifier trained with our irony dataset  All the CNN classifiers we utilize in this paper use the same parameters as BIBREF20  
Sentiment Classifier for Irony: We first implement a one-layer LSTM network to classify ironic sentences in our dataset into positive and negative ironies  The LSTM network is trained with the dataset of Semeval 2015 Task 11 BIBREF0 which is used for the sentiment analysis of figurative language in twitter  Then, we use the positive ironies and negative ironies to train the CNN sentiment classifier for irony 
Sentiment Classifier for Non-irony: Similar to the training process of the sentiment classifier for irony, we first implement a one-layer LSTM network trained with the dataset for the sentiment analysis of common twitters to classify the non-ironies into positive and negative non-ironies  Then we use the positive and negative non-ironies to train the sentiment classifier for non-irony 
Baselines
We compare our model with the following state-of-art generative models:
BackTrans BIBREF7 : In BIBREF7 , authors propose a model using machine translation in order to preserve the meaning of the sentence while reducing stylistic properties 
Unpaired BIBREF10 : In BIBREF10 , researchers implement a method to remove emotional words and add desired sentiment controlled by reinforcement learning 
CrossAlign BIBREF6 : In BIBREF6 , authors leverage refined alignment of latent representations to perform style transfer and a cross-aligned auto-encoder is implemented 
CPTG BIBREF24 : An interpolated reconstruction loss is introduced in BIBREF24 and a discriminator is implemented to control attributes in this work 
DualRL BIBREF8 : In BIBREF8 , researchers use two reinforcement rewards simultaneously to control style accuracy and content preservation 
Evaluation Metrics
In order to evaluate sentiment preservation, we use the absolute value of the difference between the standardized sentiment score of the input sentence and that of the generated sentence  We call the value as sentiment delta (senti delta)  Besides, we report the sentiment accuracy (Senti ACC) which measures whether the output sentence has the same sentiment polarity as the input sentence based on our standardized sentiment classifiers  The BLEU score BIBREF25 between the input sentences and the output sentences is calculated to evaluate the content preservation performance  In order to evaluate the overall performance of different models, we also report the geometric mean (G2) and harmonic mean (H2) of the sentiment accuracy and the BLEU score  As for the irony accuracy, we only report it in human evaluation results because it is more accurate for the human to evaluate the quality of irony as it is very complicated 
We first sample 50 non-ironic input sentences and their corresponding output sentences of different models  Then, we ask four annotators who are proficient in English to evaluate the qualities of the generated sentences of different models  They are required to rank the output sentences of our model and baselines from the best to the worst in terms of irony accuracy (Irony), Sentiment preservation (Senti) and content preservation (Content)  The best output is ranked with 1 and the worst output is ranked with 6  That means that the smaller our human evaluation value is, the better the corresponding model is 
Results and Discussions
Table TABREF35 shows the automatic evaluation results of the models in the transformation from non-ironic sentences to ironic sentences  From the results, our model obtains the best result in sentiment delta  The DualRL model achieves the highest result in other metrics, but most of its outputs are the almost same as the input sentences  So it is reasonable that DualRL system outperforms ours in these metrics but it actually does not transfer the non-ironic sentences to ironic sentences at all  From this perspective, we cannot view DualRL as an effective model for irony generation  In contrast, our model gets results close to those of DualRL and obtains a balance between irony accuracy, sentiment preservation, and content preservation if we also consider the irony accuracy discussed below 
And from human evaluation results shown in Table TABREF36 , our model gets the best average rank in irony accuracy  And as mentioned above, the DualRL model usually does not change the input sentence and outputs the same sentence  Therefore, it is reasonable that it obtains the best rank in sentiment and content preservation and ours is the second  However, it still demonstrates that our model, instead of changing nothing, transfers the style of the input sentence with content and sentiment preservation at the same time 
Case Study
In the section, we present some example outputs of different models  Table TABREF37 shows the results of the transformation from non-ironic sentences to ironic sentences  We can observe that: (1) The BackTrans system, the Unpaired system, the CrossAlign system and the CPTG system tends to generate sentences which are towards irony but do not preserve content  (2) The DualRL system preserves content and sentiment very well but even does not change the input sentence  (3) Our model considers both aspects and achieves a better balance among irony accuracy, sentiment and content preservation 
Error Analysis
Although our model outperforms other style transfer baselines according to automatic and human evaluation results, there are still some failure cases because irony generation is still a very challenging task  We would like to share the issues we meet during our experiments and our solutions to some of them in this section 
No Change: As mentioned above, many style transfer models, such as DualRL, tend to make few changes to the input sentence and output the same sentence  Actually, this is a common issue for unsupervised style transfer systems and we also meet it during our experiments  The main reason for the issue is that rewards for content preservation are too prominent and rewards for style accuracy cannot work well  In contrast, in order to guarantee the readability and fluency of the output sentence, we also cannot emphasize too much on rewards for style accuracy because it may cause some other issues such as word repetition mentioned below  A method to solve the problem is tuning hyperparameters and this is also the method we implement in this work  As for content preservation, maybe MLE methods such as back-translation are not enough because they tend to force models to generate specific words  In the future, we should further design some more suitable methods to control content preservation for models without disentangling style and content representations, such as DualRL and ours 
Word Repetition: During our experiments, we observe that some of the outputs prefer to repeat the same word as shown in Table TABREF38   This is because reinforcement learning rewards encourage the model to generate words which can get high scores from classifiers and even back-translation cannot stop it  Our solution is that we can lower the probability of decoding a word in decoders if the word has been generated in the previous time steps during testing  We also try to implement this method during training time but obtain worse performances because it may limit the effects of training  Some previous studies utilize language models to control the fluency of the output sentence and we also try this method  Nonetheless, pre-training a language model with tweets and using it to generate rewards is difficult because tweets are more casual and have more noise  Rewards from that kind of language model are usually not accurate and may confuse the model  In the future, we should come up with better methods to model language fluency with the consideration of irony accuracy, sentiment and content preservation, especially for tweets 
Improper Words: As ironic style is hard for our model to learn, it may generate some improper words which make the sentence strange  As the example shown in the Table TABREF38 , the sentiment word in the input sentence is “wonderful" and the model should change it into a negative word such as “sad" to make the output sentence ironic  However, the model changes “friday" and “fifa" which are not related to ironic styles  We have not found a very effective method to address this issue and maybe we should further explore stronger models to learn ironic styles better 
Additional Experiments
In this section, we describe some additional experiments on the transformation from ironic sentences to non-ironic sentences  Sometimes ironies are hard to understand and may cause misunderstanding, for which our task also explores the transformation from ironic sentences to non-ironic sentences 
As shown in Table TABREF46 , we also conduct automatic evaluations and the conclusions are similar to those of the transformation from non-ironic sentences to ironic sentences  As for human evaluation results in Table TABREF47 , our model still can achieve the second-best results in sentiment and content preservation  Nevertheless, DualRL system and ours get poor performances in irony accuracy  The reason may be that the other four baselines tend to generate common and even not fluent sentences which are irrelevant to the input sentences and are hard to be identified as ironies  So annotators usually mark these output sentences as non-ironic sentences, which causes these models to obtain better performances than DualRL and ours but much poorer results in sentiment and content preservation  Some examples are shown in Table TABREF52  
Conclusion and Future Work
In this paper, we first systematically define irony generation based on style transfer  Because of the lack of irony data, we make use of twitter and build a large-scale dataset  In order to control irony accuracy, sentiment preservation and content preservation at the same time, we also design a combination of rewards for reinforcement learning and incorporate reinforcement learning with a pre-training process  Experimental results demonstrate that our model outperforms other generative models and our rewards are effective  Although our model design is effective, there are still many errors and we systematically analyze them  In the future, we are interested in exploring these directions and our work may extend to other kinds of ironies which are more difficult to model 

ground_truth: Irony Classifier, Sentiment Classifier for Irony, Sentiment Classifier for Non-irony, transformation from ironic sentences to non-ironic sentences

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:  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