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 recall score?
Context 1: 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 
Context 2: Introduction
Word Sense Disambiguation (WSD) is a fundamental task and long-standing challenge in Natural Language Processing (NLP), which aims to find the exact sense of an ambiguous word in a particular context BIBREF0  Previous WSD approaches can be grouped into two main categories: knowledge-based and supervised methods 
Knowledge-based WSD methods rely on lexical resources like WordNet BIBREF1 and usually exploit two kinds of lexical knowledge  The gloss, which defines a word sense meaning, is first utilized in Lesk algorithm BIBREF2 and then widely taken into account in many other approaches BIBREF3, BIBREF4  Besides, structural properties of semantic graphs are mainly used in graph-based algorithms BIBREF5, BIBREF6 
Traditional supervised WSD methods BIBREF7, BIBREF8, BIBREF9 focus on extracting manually designed features and then train a dedicated classifier (word expert) for every target lemma 
Although word expert supervised WSD methods perform better, they are less flexible than knowledge-based methods in the all-words WSD task BIBREF10  Recent neural-based methods are devoted to dealing with this problem  BIBREF11 present a supervised classifier based on Bi-LSTM, which shares parameters among all word types except the last layer  BIBREF10 convert WSD task to a sequence labeling task, thus building a unified model for all polysemous words  However, neither of them can totally beat the best word expert supervised methods 
More recently, BIBREF12 propose to leverage the gloss information from WordNet and model the semantic relationship between the context and gloss in an improved memory network  Similarly, BIBREF13 introduce a (hierarchical) co-attention mechanism to generate co-dependent representations for the context and gloss  Their attempts prove that incorporating gloss knowledge into supervised WSD approach is helpful, but they still have not achieved much improvement, because they may not make full use of gloss knowledge 
In this paper, we focus on how to better leverage gloss information in a supervised neural WSD system  Recently, the pre-trained language models, such as ELMo BIBREF14 and BERT BIBREF15, have shown their effectiveness to alleviate the effort of feature engineering  Especially, BERT has achieved excellent results in question answering (QA) and natural language inference (NLI)  We construct context-gloss pairs from glosses of all possible senses (in WordNet) of the target word, thus treating WSD task as a sentence-pair classification problem  We fine-tune the pre-trained BERT model and achieve new state-of-the-art results on WSD task  In particular, our contribution is two-fold:
1  We construct context-gloss pairs and propose three BERT-based models for WSD 
2  We fine-tune the pre-trained BERT model, and the experimental results on several English all-words WSD benchmark datasets show that our approach significantly outperforms the state-of-the-art systems 
Methodology
In this section, we describe our method in detail 
Methodology ::: Task Definition
In WSD, a sentence $s$ usually consists of a series of words: $\lbrace w_1,\cdots ,w_m\rbrace $, and some of the words $\lbrace w_{i_1},\cdots ,w_{i_k}\rbrace $ are targets $\lbrace t_1,\cdots ,t_k\rbrace $ need to be disambiguated  For each target $t$, its candidate senses $\lbrace c_1,\cdots ,c_n\rbrace $ come from entries of its lemma in a pre-defined sense inventory (usually WordNet)  Therefore, WSD task aims to find the most suitable entry (symbolized as unique sense key) for each target in a sentence  See a sentence example in Table TABREF1 
Methodology ::: BERT
BERT BIBREF15 is a new language representation model, and its architecture is a multi-layer bidirectional Transformer encoder  BERT model is pre-trained on a large corpus and two novel unsupervised prediction tasks, i e , masked language model and next sentence prediction tasks are used in pre-training  When incorporating BERT into downstream tasks, the fine-tuning procedure is recommended  We fine-tune the pre-trained BERT model on WSD task 
Methodology ::: BERT ::: BERT(Token-CLS)
Since every target in a sentence needs to be disambiguated to find its exact sense, WSD task can be regarded as a token-level classification task  To incorporate BERT to WSD task, we take the final hidden state of the token corresponding to the target word (if more than one token, we average them) and add a classification layer for every target lemma, which is the same as the last layer of the Bi-LSTM model BIBREF11 
Methodology ::: GlossBERT
BERT can explicitly model the relationship of a pair of texts, which has shown to be beneficial to many pair-wise natural language understanding tasks  In order to fully leverage gloss information, we propose GlossBERT to construct context-gloss pairs from all possible senses of the target word in WordNet, thus treating WSD task as a sentence-pair classification problem 
We describe our construction method with an example (See Table TABREF1)  There are four targets in this sentence, and here we take target word research as an example:
Methodology ::: GlossBERT ::: Context-Gloss Pairs
The sentence containing target words is denoted as context sentence  For each target word, we extract glosses of all $N$ possible senses (here $N=4$) of the target word (research) in WordNet to obtain the gloss sentence  [CLS] and [SEP] marks are added to the context-gloss pairs to make it suitable for the input of BERT model  A similar idea is also used in aspect-based sentiment analysis BIBREF16 
Methodology ::: GlossBERT ::: Context-Gloss Pairs with Weak Supervision
Based on the previous construction method, we add weak supervised signals to the context-gloss pairs (see the highlighted part in Table TABREF1)  The signal in the gloss sentence aims to point out the target word, and the signal in the context sentence aims to emphasize the target word considering the situation that a target word may occur more than one time in the same sentence 
Therefore, each target word has $N$ context-gloss pair training instances ($label\in \lbrace yes, no\rbrace $)  When testing, we output the probability of $label=yes$ of each context-gloss pair and choose the sense corresponding to the highest probability as the prediction label of the target word  We experiment with three GlossBERT models:
Methodology ::: GlossBERT ::: GlossBERT(Token-CLS)
We use context-gloss pairs as input  We highlight the target word by taking the final hidden state of the token corresponding to the target word (if more than one token, we average them) and add a classification layer ($label\in \lbrace yes, no\rbrace $) 
Methodology ::: GlossBERT ::: GlossBERT(Sent-CLS)
We use context-gloss pairs as input  We take the final hidden state of the first token [CLS] as the representation of the whole sequence and add a classification layer ($label\in \lbrace yes, no\rbrace $), which does not highlight the target word 
Methodology ::: GlossBERT ::: GlossBERT(Sent-CLS-WS)
We use context-gloss pairs with weak supervision as input  We take the final hidden state of the first token [CLS] and add a classification layer ($label\in \lbrace yes, no\rbrace $), which weekly highlight the target word by the weak supervision 
Experiments ::: Datasets
The statistics of the WSD datasets are shown in Table TABREF12 
Experiments ::: Datasets ::: Training Dataset
Following previous work BIBREF13, BIBREF12, BIBREF10, BIBREF17, BIBREF9, BIBREF7, we choose SemCor3 0 as training corpus, which is the largest corpus manually annotated with WordNet sense for WSD 
Experiments ::: Datasets ::: Evaluation Datasets
We evaluate our method on several English all-words WSD datasets  For a fair comparison, we use the benchmark datasets proposed by BIBREF17 which include five standard all-words fine-grained WSD datasets from the Senseval and SemEval competitions: Senseval-2 (SE2), Senseval-3 (SE3), SemEval-2007 (SE07), SemEval-2013 (SE13) and SemEval-2015 (SE15)  Following BIBREF13, BIBREF12 and BIBREF10, we choose SE07, the smallest among these test sets, as the development set 
Experiments ::: Datasets ::: WordNet
Since BIBREF17 map all the sense annotations in these datasets from their original versions to WordNet 3 0, we extract word sense glosses from WordNet 3 0 
Experiments ::: Settings
We use the pre-trained uncased BERT$_\mathrm {BASE}$ model for fine-tuning, because we find that BERT$_\mathrm {LARGE}$ model performs slightly worse than BERT$_\mathrm {BASE}$ in this task  The number of Transformer blocks is 12, the number of the hidden layer is 768, the number of self-attention heads is 12, and the total number of parameters of the pre-trained model is 110M  When fine-tuning, we use the development set (SE07) to find the optimal settings for our experiments  We keep the dropout probability at 0 1, set the number of epochs to 4  The initial learning rate is 2e-5, and the batch size is 64 
Experiments ::: Results
Table TABREF19 shows the performance of our method on the English all-words WSD benchmark datasets  We compare our approach with previous methods 
The first block shows the MFS baseline, which selects the most frequent sense in the training corpus for each target word 
The second block shows two knowledge-based systems  Lesk$_{ext+emb}$ BIBREF4 is a variant of Lesk algorithm BIBREF2 by calculating the gloss-context overlap of the target word  Babelfy BIBREF6 is a unified graph-based approach which exploits the semantic network structure from BabelNet 
The third block shows two word expert traditional supervised systems  IMS BIBREF7 is a flexible framework which trains SVM classifiers and uses local features  And IMS$_{+emb}$ BIBREF9 is the best configuration of the IMS framework, which also integrates word embeddings as features 
The fourth block shows several recent neural-based methods  Bi-LSTM BIBREF11 is a baseline for neural models  Bi-LSTM$_{+ att  + LEX + POS}$ BIBREF10 is a multi-task learning framework for WSD, POS tagging, and LEX with self-attention mechanism, which converts WSD to a sequence learning task  GAS$_{ext}$ BIBREF12 is a variant of GAS which is a gloss-augmented variant of the memory network by extending gloss knowledge  CAN$^s$ and HCAN BIBREF13 are sentence-level and hierarchical co-attention neural network models which leverage gloss knowledge 
In the last block, we report the performance of our method  BERT(Token-CLS) is our baseline, which does not incorporate gloss information, and it performs slightly worse than previous traditional supervised methods and recent neural-based methods  It proves that directly using BERT cannot obtain performance growth  The other three methods outperform other models by a substantial margin, which proves that the improvements come from leveraging BERT to better exploit gloss information  It is worth noting that our method achieves significant improvements in SE07 and Verb over previous methods, which have the highest ambiguity level among all datasets and all POS tags respectively according to BIBREF17 
Moreover, GlossBERT(Token-CLS) performs better than GlossBERT(Sent-CLS), which proves that highlighting the target word in the sentence is important  However, the weakly highlighting method GlossBERT(Sent-CLS-WS) performs best in most circumstances, which may result from its combination of the advantages of the other two methods 
Experiments ::: Discussion
There are two main reasons for the great improvements of our experimental results  First, we construct context-gloss pairs and convert WSD problem to a sentence-pair classification task which is similar to NLI tasks and train only one classifier, which is equivalent to expanding the corpus  Second, we leverage BERT BIBREF15 to better exploit the gloss information  BERT model shows its advantage in dealing with sentence-pair classification tasks by its amazing improvement on QA and NLI tasks  This advantage comes from both of its two novel unsupervised prediction tasks 
Compared with traditional word expert supervised methods, our GlossBERT shows its effectiveness to alleviate the effort of feature engineering and does not require training a dedicated classifier for every target lemma  Up to now, it can be said that the neural network method can totally beat the traditional word expert method  Compared with recent neural-based methods, our solution is more intuitive and can make better use of gloss knowledge  Besides, our approach demonstrates that when we fine-tune BERT on a downstream task, converting it into a sentence-pair classification task may be a good choice 
Conclusion
In this paper, we seek to better leverage gloss knowledge in a supervised neural WSD system  We propose a new solution to WSD by constructing context-gloss pairs and then converting WSD to a sentence-pair classification task  We fine-tune the pre-trained BERT model and achieve new state-of-the-art results on WSD task 
Acknowledgments
We would like to thank the anonymous reviewers for their valuable comments  The research work is supported by National Natural Science Foundation of China (No  61751201 and 61672162), Shanghai Municipal Science and Technology Commission (16JC1420401 and 17JC1404100), Shanghai Municipal Science and Technology Major Project (No 2018SHZDZX01) and ZJLab 
Context 3: Introduction
Data annotation is a major bottleneck for the application of supervised learning approaches to many problems  As a result, unsupervised methods that learn directly from unlabeled data are increasingly important  For tasks related to unsupervised syntactic analysis, discrete generative models have dominated in recent years – for example, for both part-of-speech (POS) induction BIBREF0 , BIBREF1 and unsupervised dependency parsing BIBREF2 , BIBREF3 , BIBREF4   While similar models have had success on a range of unsupervised tasks, they have mostly ignored the apparent utility of continuous word representations evident from supervised NLP applications BIBREF5 , BIBREF6   In this work, we focus on leveraging and explicitly representing continuous word embeddings within unsupervised models of syntactic structure 
Pre-trained word embeddings from massive unlabeled corpora offer a compact way of injecting a prior notion of word similarity into models that would otherwise treat words as discrete, isolated categories  However, the specific properties of language captured by any particular embedding scheme can be difficult to control, and, further, may not be ideally suited to the task at hand  For example, pre-trained skip-gram embeddings BIBREF7 with small context window size are found to capture the syntactic properties of language well BIBREF8 , BIBREF9   However, if our goal is to separate syntactic categories, this embedding space is not ideal – POS categories correspond to overlapping interspersed regions in the embedding space, evident in Figure SECREF4  
In our approach, we propose to learn a new latent embedding space as a projection of pre-trained embeddings (depicted in Figure SECREF5 ), while jointly learning latent syntactic structure – for example, POS categories or syntactic dependencies  To this end, we introduce a new generative model (shown in Figure FIGREF6 ) that first generates a latent syntactic representation (e g  a dependency parse) from a discrete structured prior (which we also call the “syntax model”), then, conditioned on this representation, generates a sequence of latent embedding random variables corresponding to each word, and finally produces the observed (pre-trained) word embeddings by projecting these latent vectors through a parameterized non-linear function  The latent embeddings can be jointly learned with the structured syntax model in a completely unsupervised fashion 
By choosing an invertible neural network as our non-linear projector, and then parameterizing our model in terms of the projection's inverse, we are able to derive tractable exact inference and marginal likelihood computation procedures so long as inference is tractable in the underlying syntax model  In sec:learn-with-inv we show that this derivation corresponds to an alternate view of our approach whereby we jointly learn a mapping of observed word embeddings to a new embedding space that is more suitable for the syntax model, but include an additional Jacobian regularization term to prevent information loss 
Recent work has sought to take advantage of word embeddings in unsupervised generative models with alternate approaches BIBREF9 , BIBREF10 , BIBREF11 , BIBREF12   BIBREF9 build an HMM with Gaussian emissions on observed word embeddings, but they do not attempt to learn new embeddings  BIBREF10 , BIBREF11 , and BIBREF12 extend HMM or dependency model with valence (DMV) BIBREF2 with multinomials that use word (or tag) embeddings in their parameterization  However, they do not represent the embeddings as latent variables 
In experiments, we instantiate our approach using both a Markov-structured syntax model and a tree-structured syntax model – specifically, the DMV  We evaluate on two tasks: part-of-speech (POS) induction and unsupervised dependency parsing without gold POS tags  Experimental results on the Penn Treebank BIBREF13 demonstrate that our approach improves the basic HMM and DMV by a large margin, leading to the state-of-the-art results on POS induction, and state-of-the-art results on unsupervised dependency parsing in the difficult training scenario where neither gold POS annotation nor punctuation-based constraints are available 
Model
As an illustrative example, we first present a baseline model for Markov syntactic structure (POS induction) that treats a sequence of pre-trained word embeddings as observations  Then, we propose our novel approach, again using Markov structure, that introduces latent word embedding variables and a neural projector  Lastly, we extend our approach to more general syntactic structures 
Example: Gaussian HMM
We start by describing the Gaussian hidden Markov model introduced by BIBREF9 , which is a locally normalized model with multinomial transitions and Gaussian emissions  Given a sentence of length INLINEFORM0 , we denote the latent POS tags as INLINEFORM1 , observed (pre-trained) word embeddings as INLINEFORM2 , transition parameters as INLINEFORM3 , and Gaussian emission parameters as INLINEFORM4   The joint distribution of data and latent variables factors as:
DISPLAYFORM0
where INLINEFORM0 is the multinomial transition probability and INLINEFORM1 is the multivariate Gaussian emission probability 
While the observed word embeddings do inform this model with a notion of word similarity – lacking in the basic multinomial HMM – the Gaussian emissions may not be sufficiently flexible to separate some syntactic categories in the complex pre-trained embedding space – for example the skip-gram embedding space as visualized in Figure SECREF4 where different POS categories overlap  Next we introduce a new approach that adds flexibility to the emission distribution by incorporating new latent embedding variables 
Markov Structure with Neural Projector
To flexibly model observed embeddings and yield a new representation space that is more suitable for the syntax model, we propose to cascade a neural network as a projection function, deterministically transforming the simple space defined by the Gaussian HMM to the observed embedding space  We denote the latent embedding of the INLINEFORM0 word in a sentence as INLINEFORM1 , and the neural projection function as INLINEFORM2 , parameterized by INLINEFORM3   In the case of sequential Markov structure, our new model corresponds to the following generative process:
For each time step INLINEFORM0 ,
[noitemsep, leftmargin=*]
Draw the latent state INLINEFORM0
Draw the latent embedding INLINEFORM0
Deterministically produce embedding
INLINEFORM0
The graphical model is depicted in Figure FIGREF6   The deterministic projection can also be viewed as sampling each observation from a point mass at INLINEFORM0   The joint distribution of our model is: DISPLAYFORM0
where INLINEFORM0 is a conditional Gaussian distribution, and INLINEFORM1 is the Dirac delta function centered at INLINEFORM2 : DISPLAYFORM0
General Structure with Neural Projector
Our approach can be applied to a broad family of structured syntax models  We denote latent embedding variables as INLINEFORM0 , discrete latent variables in the syntax model as INLINEFORM1 ( INLINEFORM2 ), where INLINEFORM3 are conditioned to generate INLINEFORM4   The joint probability of our model factors as:
DISPLAYFORM0
where INLINEFORM0 represents the probability of the syntax model, and can encode any syntactic structure – though, its factorization structure will determine whether inference is tractable in our full model  As shown in Figure FIGREF6 , we focus on two syntax models for syntactic analysis in this paper  The first is Markov-structured, which we use for POS induction, and the second is DMV-structured, which we use to learn dependency parses without supervision 
The marginal data likelihood of our model is: DISPLAYFORM0
While the discrete variables INLINEFORM0 can be marginalized out with dynamic program in many cases, it is generally intractable to marginalize out the latent continuous variables, INLINEFORM1 , for an arbitrary projection INLINEFORM2 in Eq  ( EQREF17 ), which means inference and learning may be difficult  In sec:opt, we address this issue by constraining INLINEFORM3 to be invertible, and show that this constraint enables tractable exact inference and marginal likelihood computation 
Learning & Inference
In this section, we introduce an invertibility condition for our neural projector to tackle the optimization challenge  Specifically, we constrain our neural projector with two requirements: (1) INLINEFORM0 and (2) INLINEFORM1 exists  Invertible transformations have been explored before in independent components analysis BIBREF14 , gaussianization BIBREF15 , and deep density models BIBREF16 , BIBREF17 , BIBREF18 , for unstructured data  Here, we generalize this style of approach to structured learning, and augment it with discrete latent variables ( INLINEFORM2 )  Under the invertibility condition, we derive a learning algorithm and give another view of our approach revealed by the objective function  Then, we present the architecture of a neural projector we use in experiments: a volume-preserving invertible neural network proposed by BIBREF16 for independent components estimation 
Learning with Invertibility
For ease of exposition, we explain the learning algorithm in terms of Markov structure without loss of generality  As shown in Eq  ( EQREF17 ), the optimization challenge in our approach comes from the intractability of the marginalized emission factor INLINEFORM0   If we can marginalize out INLINEFORM1 and compute INLINEFORM2 , then the posterior and marginal likelihood of our Markov-structured model can be computed with the forward-backward algorithm  We can apply Eq  ( EQREF14 ) and obtain : INLINEFORM3
By using the change of variable rule to the integration, which allows the integration variable INLINEFORM0 to be replaced by INLINEFORM1 , the marginal emission factor can be computed in closed-form when the invertibility condition is satisfied: DISPLAYFORM0
where INLINEFORM0 is a conditional Gaussian distribution, INLINEFORM1 is the Jacobian matrix of function INLINEFORM2 at INLINEFORM3 , and INLINEFORM4 represents the absolute value of its determinant  This Jacobian term is nonzero and differentiable if and only if INLINEFORM5 exists 
Eq  ( EQREF19 ) shows that we can directly calculate the marginal emission distribution INLINEFORM0   Denote the marginal data likelihood of Gaussian HMM as INLINEFORM1 , then the log marginal data likelihood of our model can be directly written as: DISPLAYFORM0
where INLINEFORM0 represents the new sequence of embeddings after applying INLINEFORM1 to each INLINEFORM2   Eq  ( EQREF20 ) shows that the training objective of our model is simply the Gaussian HMM log likelihood with an additional Jacobian regularization term  From this view, our approach can be seen as equivalent to reversely projecting the data through INLINEFORM3 to another manifold INLINEFORM4 that is directly modeled by the Gaussian HMM, with a regularization term  Intuitively, we optimize the reverse projection INLINEFORM5 to modify the INLINEFORM6 space, making it more appropriate for the syntax model  The Jacobian regularization term accounts for the volume expansion or contraction behavior of the projection  Maximizing it can be thought of as preventing information loss  In the extreme case, the Jacobian determinant is equal to zero, which means the projection is non-invertible and thus information is being lost through the projection

ground_truth: 0.7033

0.7033

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. Is SemCor3.0 reflective of English language data in general?
Context 3:  Such “information preserving” regularization is crucial during optimization, otherwise the trivial solution of always projecting data to the same single point to maximize likelihood is viable 
More generally, for an arbitrary syntax model the data likelihood of our approach is: DISPLAYFORM0
If the syntax model itself allows for tractable inference and marginal likelihood computation, the same dynamic program can be used to marginalize out INLINEFORM0   Therefore, our joint model inherits the tractability of the underlying syntax model 
Invertible Volume-Preserving Neural Net
For the projection we can use an arbitrary invertible function, and given the representational power of neural networks they seem a natural choice  However, calculating the inverse and Jacobian of an arbitrary neural network can be difficult, as it requires that all component functions be invertible and also requires storage of large Jacobian matrices, which is memory intensive  To address this issue, several recent papers propose specially designed invertible networks that are easily trainable yet still powerful BIBREF16 , BIBREF17 , BIBREF19   Inspired by these works, we use the invertible transformation proposed by BIBREF16 , which consists of a series of “coupling layers”  This architecture is specially designed to guarantee a unit Jacobian determinant (and thus the invertibility property) 
From Eq  ( EQREF22 ) we know that only INLINEFORM0 is required for accomplishing learning and inference; we never need to explicitly construct INLINEFORM1   Thus, we directly define the architecture of INLINEFORM2   As shown in Figure FIGREF24 , the nonlinear transformation from the observed embedding INLINEFORM3 to INLINEFORM4 represents the first coupling layer  The input in this layer is partitioned into left and right halves of dimensions, INLINEFORM5 and INLINEFORM6 , respectively  A single coupling layer is defined as: DISPLAYFORM0
where INLINEFORM0 is the coupling function and can be any nonlinear form  This transformation satisfies INLINEFORM1 , and BIBREF16 show that its Jacobian matrix is triangular with all ones on the main diagonal  Thus the Jacobian determinant is always equal to one (i e  volume-preserving) and the invertibility condition is naturally satisfied 
To be sufficiently expressive, we compose multiple coupling layers as suggested in BIBREF16   Specifically, we exchange the role of left and right half vectors at each layer as shown in Figure FIGREF24   For instance, from INLINEFORM0 to INLINEFORM1 the left subset INLINEFORM2 is unchanged, while from INLINEFORM3 to INLINEFORM4 the right subset INLINEFORM5 remains the same  Also note that composing multiple coupling layers does not change the volume-preserving and invertibility properties  Such a sequence of invertible transformations from the data space INLINEFORM6 to INLINEFORM7 is also called normalizing flow BIBREF20  
Experiments
In this section, we first describe our datasets and experimental setup  We then instantiate our approach with Markov and DMV-structured syntax models, and report results on POS tagging and dependency grammar induction respectively  Lastly, we analyze the learned latent embeddings 
Data
For both POS tagging and dependency parsing, we run experiments on the Wall Street Journal (WSJ) portion of the Penn Treebank  To create the observed data embeddings, we train skip-gram word embeddings BIBREF7 that are found to capture syntactic properties well when trained with small context window BIBREF8 , BIBREF9   Following BIBREF9 , the dimensionality INLINEFORM0 is set to 100, and the training context window size is set to 1 to encode more syntactic information  The skip-gram embeddings are trained on the one billion word language modeling benchmark dataset BIBREF21 in addition to the WSJ corpus 
General Experimental Setup
For the neural projector, we employ rectified networks as coupling function INLINEFORM0 following BIBREF16   We use a rectified network with an input layer, one hidden layer, and linear output units, the number of hidden units is set to the same as the number of input units  The number of coupling layers are varied as 4, 8, 16 for both tasks  We optimize marginal data likelihood directly using Adam BIBREF22   For both tasks in the fully unsupervised setting, we do not tune the hyper-parameters using supervised data 
Unsupervised POS tagging
For unsupervised POS tagging, we use a Markov-structured syntax model in our approach, which is a popular structure for unsupervised tagging tasks BIBREF9 , BIBREF10  
Following existing literature, we train and test on the entire WSJ corpus (49208 sentences, 1M tokens)  We use 45 tag clusters, the number of POS tags that appear in WSJ corpus  We train the discrete HMM and the Gaussian HMM BIBREF9 as baselines  For the Gaussian HMM, mean vectors of Gaussian emissions are initialized with the empirical mean of all word vectors with an additive noise  We assume diagonal covariance matrix for INLINEFORM0 and initialize it with the empirical variance of the word vectors  Following BIBREF9 , the covariance matrix is fixed during training  The multinomial probabilities are initialized as INLINEFORM1 , where INLINEFORM2   For our approach, we initialize the syntax model and Gaussian parameters with the pre-trained Gaussian HMM  The weights of layers in the rectified network are initialized from a uniform distribution with mean zero and a standard deviation of INLINEFORM3 , where INLINEFORM4 is the input dimension  We evaluate the performance of POS tagging with both Many-to-One (M-1) accuracy BIBREF23 and V-Measure (VM) BIBREF24   Given a model we found that the tagging performance is well-correlated with the training data likelihood, thus we use training data likelihood as a unsupervised criterion to select the trained model over 10 random restarts after training 50 epochs  We repeat this process 5 times and report the mean and standard deviation of performance 
We compare our approach with basic HMM, Gaussian HMM, and several state-of-the-art systems, including sophisticated HMM variants and clustering techniques with hand-engineered features  The results are presented in Table TABREF32   Through the introduced latent embeddings and additional neural projection, our approach improves over the Gaussian HMM by 5 4 points in M-1 and 5 6 points in VM  Neural HMM (NHMM) BIBREF10 is a baseline that also learns word representation jointly  Both their basic model and extended Conv version does not outperform the Gaussian HMM  Their best model incorporates another LSTM to model long distance dependency and breaks the Markov assumption, yet our approach still achieves substantial improvement over it without considering more context information  Moreover, our method outperforms the best published result that benefits from hand-engineered features BIBREF27 by 2 0 points on VM 
We found that most tagging errors happen in noun subcategories  Therefore, we do the one-to-one mapping between gold POS tags and induced clusters and plot the normalized confusion matrix of noun subcategories in Figure FIGREF35   The Gaussian HMM fails to identify “NN” and “NNS” correctly for most cases, and it often recognizes “NNPS” as “NNP”  In contrast, our approach corrects these errors well 
Unsupervised Dependency Parsing without gold POS tags
For the task of unsupervised dependency parse induction, we employ the Dependency Model with Valence (DMV) BIBREF2 as the syntax model in our approach  DMV is a generative model that defines a probability distribution over dependency parse trees and syntactic categories, generating tokens and dependencies in a head-outward fashion  While, traditionally, DMV is trained using gold POS tags as observed syntactic categories, in our approach, we treat each tag as a latent variable, as described in sec:general-neural 
Most existing approaches to this task are not fully unsupervised since they rely on gold POS tags following the original experimental setup for DMV

ground_truth: Yes

Unanswerable

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 is the invertibility condition?
Context 3:  This is partially because automatically parsing from words is difficult even when using unsupervised syntactic categories BIBREF29   However, inducing dependencies from words alone represents a more realistic experimental condition since gold POS tags are often unavailable in practice  Previous work that has trained from words alone often requires additional linguistic constraints (like sentence internal boundaries) BIBREF29 , BIBREF30 , BIBREF31 , BIBREF32 , acoustic cues BIBREF33 , additional training data BIBREF4 , or annotated data from related languages BIBREF34   Our approach is naturally designed to train on word embeddings directly, thus we attempt to induce dependencies without using gold POS tags or other extra linguistic information 
Like previous work we use sections 02-21 of WSJ corpus as training data and evaluate on section 23, we remove punctuations and train the models on sentences of length INLINEFORM0 , “head-percolation” rules BIBREF39 are applied to obtain gold dependencies for evaluation  We train basic DMV, extended DMV (E-DMV) BIBREF35 and Gaussian DMV (which treats POS tag as unknown latent variables and generates observed word embeddings directly conditioned on them following Gaussian distribution) as baselines  Basic DMV and E-DMV are trained with Viterbi EM BIBREF40 on unsupervised POS tags induced from our Markov-structured model described in sec:pos  Multinomial parameters of the syntax model in both Gaussian DMV and our model are initialized with the pre-trained DMV baseline  Other parameters are initialized in the same way as in the POS tagging experiment  The directed dependency accuracy (DDA) is used for evaluation and we report accuracy on sentences of length INLINEFORM1 and all lengths  We train the parser until training data likelihood converges, and report the mean and standard deviation over 20 random restarts 
Our model directly observes word embeddings and does not require gold POS tags during training  Thus, results from related work trained on gold tags are not directly comparable  However, to measure how these systems might perform without gold tags, we run three recent state-of-the-art systems in our experimental setting: UR-A E-DMV BIBREF36 , Neural E-DMV BIBREF11 , and CRF Autoencoder (CRFAE) BIBREF37   We use unsupervised POS tags (induced from our Markov-structured model) in place of gold tags  We also train basic DMV on gold tags and include several state-of-the-art results on gold tags as reference points 
As shown in Table TABREF39 , our approach is able to improve over the Gaussian DMV by 4 8 points on length INLINEFORM0 and 4 8 points on all lengths, which suggests the additional latent embedding layer and neural projector are helpful  The proposed approach yields, to the best of our knowledge, state-of-the-art performance without gold POS annotation and without sentence-internal boundary information  DMV, UR-A E-DMV, Neural E-DMV, and CRFAE suffer a large decrease in performance when trained on unsupervised tags – an effect also seen in previous work BIBREF29 , BIBREF34   Since our approach induces latent POS tags jointly with dependency trees, it may be able to learn POS clusters that are more amenable to grammar induction than the unsupervised tags  We observe that CRFAE underperforms its gold-tag counterpart substantially  This may largely be a result of the model's reliance on prior linguistic rules that become unavailable when gold POS tag types are unknown  Many extensions to DMV can be considered orthogonal to our approach – they essentially focus on improving the syntax model  It is possible that incorporating these more sophisticated syntax models into our approach may lead to further improvements 
Sensitivity Analysis
In the above experiments we initialize the structured syntax components with the pre-trained Gaussian or discrete baseline, which is shown as a useful technique to help train our deep models  We further study the results with fully random initialization  In the POS tagging experiment, we report the results in Table TABREF48   While the performance with 4 layers is comparable to the pre-trained Gaussian initialization, deeper projections (8 or 16 layers) result in a dramatic drop in performance  This suggests that the structured syntax model with very deep projections is difficult to train from scratch, and a simpler projection might be a good compromise in the random initialization setting 
Different from the Markov prior in POS tagging experiments, our parsing model seems to be quite sensitive to the initialization  For example, directed accuracy of our approach on sentences of length INLINEFORM0 is below 40 0 with random initialization  This is consistent with previous work that has noted the importance of careful initialization for DMV-based models such as the commonly used harmonic initializer BIBREF2   However, it is not straightforward to apply the harmonic initializer for DMV directly in our model without using some kind of pre-training since we do not observe gold POS 
We investigate the effect of the choice of pre-trained embedding on performance while using our approach  To this end, we additionally include results using fastText embeddings BIBREF41 – which, in contrast with skip-gram embeddings, include character-level information  We set the context windows size to 1 and the dimension size to 100 as in the skip-gram training, while keeping other parameters set to their defaults  These results are summarized in Table TABREF50 and Table TABREF51   While fastText embeddings lead to reduced performance with our model, our approach still yields an improvement over the Gaussian baseline with the new observed embeddings space 
Qualitative Analysis of Embeddings
We perform qualitative analysis to understand how the latent embeddings help induce syntactic structures  First we filter out low-frequency words and punctuations in WSJ, and visualize the rest words (10k) with t-SNE BIBREF42 under different embeddings  We assign each word with its most likely gold POS tags in WSJ and color them according to the gold POS tags 
For our Markov-structured model, we have displayed the embedding space in Figure SECREF5 , where the gold POS clusters are well-formed  Further, we present five example target words and their five nearest neighbors in terms of cosine similarity  As shown in Table TABREF53 , the skip-gram embedding captures both semantic and syntactic aspects to some degree, yet our embeddings are able to focus especially on the syntactic aspects of words, in an unsupervised fashion without using any extra morphological information 
In Figure FIGREF54 we depict the learned latent embeddings with the DMV-structured syntax model  Unlike the Markov structure, the DMV structure maps a large subset of singular and plural nouns to the same overlapping region  However, two clusters of singular and plural nouns are actually separated  We inspect the two clusters and the overlapping region in Figure FIGREF54 , it turns out that the nouns in the separated clusters are words that can appear as subjects and, therefore, for which verb agreement is important to model  In contrast, the nouns in the overlapping region are typically objects  This demonstrates that the latent embeddings are focusing on aspects of language that are specifically important for modeling dependency without ever having seen examples of dependency parses  Some previous work has deliberately created embeddings to capture different notions of similarity BIBREF43 , BIBREF44 , while they use extra morphology or dependency annotations to guide the embedding learning, our approach provides a potential alternative to create new embeddings that are guided by structured syntax model, only using unlabeled text corpora 
Related Work
Our approach is related to flow-based generative models, which are first described in NICE BIBREF16 and have recently received more attention BIBREF17 , BIBREF19 , BIBREF18   This relevant work mostly adopts simple (e g  Gaussian) and fixed priors and does not attempt to learn interpretable latent structures  Another related generative model class is variational auto-encoders (VAEs) BIBREF45 that optimize a lower bound on the marginal data likelihood, and can be extended to learn latent structures BIBREF46 , BIBREF47   Against the flow-based models, VAEs remove the invertibility constraint but sacrifice the merits of exact inference and exact log likelihood computation, which potentially results in optimization challenges BIBREF48   Our approach can also be viewed in connection with generative adversarial networks (GANs) BIBREF49 that is a likelihood-free framework to learn implicit generative models  However, it is non-trivial for a gradient-based method like GANs to propagate gradients through discrete structures 
Conclusion
In this work, we define a novel generative approach to leverage continuous word representations for unsupervised learning of syntactic structure  Experiments on both POS induction and unsupervised dependency parsing tasks demonstrate the effectiveness of our proposed approach  Future work might explore more sophisticated invertible projections, or recurrent projections that jointly transform the entire input sequence 

ground_truth: The neural projector must be invertible.

we constrain our neural projector with two requirements: (1) INLINEFORM0 and (2) INLINEFORM1 exists