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. Does their NER model learn NER from both text and images?
Context 1: Introduction
Social media with abundant user-generated posts provide a rich platform for understanding events, opinions and preferences of groups and individuals  These insights are primarily hidden in unstructured forms of social media posts, such as in free-form text or images without tags  Named entity recognition (NER), the task of recognizing named entities from free-form text, is thus a critical step for building structural information, allowing for its use in personalized assistance, recommendations, advertisement, etc 
While many previous approaches BIBREF0 , BIBREF1 , BIBREF2 , BIBREF3 on NER have shown success for well-formed text in recognizing named entities via word context resolution (e g  LSTM with word embeddings) combined with character-level features (e g  CharLSTM/CNN), several additional challenges remain for recognizing named entities from extremely short and coarse text found in social media posts  For instance, short social media posts often do not provide enough textual contexts to resolve polysemous entities (e g  “monopoly is da best ", where `monopoly' may refer to a board game (named entity) or a term in economics)  In addition, noisy text includes a huge number of unknown tokens due to inconsistent lexical notations and frequent mentions of various newly trending entities (e g  “xoxo Marshmelloooo ", where `Marshmelloooo' is a mis-spelling of a known entity `Marshmello', a music producer), making word embeddings based neural networks NER models vulnerable 
To address the challenges above for social media posts, we build upon the state-of-the-art neural architecture for NER with the following two novel approaches (Figure FIGREF1 )  First, we propose to leverage auxiliary modalities for additional context resolution of entities  For example, many popular social media platforms now provide ways to compose a post in multiple modalities - specifically image and text (e g  Snapchat captions, Twitter posts with image URLs), from which we can obtain additional context for understanding posts  While “monopoly" in the previous example is ambiguous in its textual form, an accompanying snap image of a board game can help disambiguate among polysemous entities, thereby correctly recognizing it as a named entity 
Second, we also propose a general modality attention module which chooses per decoding step the most informative modality among available ones (in our case, word embeddings, character embeddings, or visual features) to extract context from  For example, the modality attention module lets the decoder attenuate the word-level signals for unknown word tokens (“Marshmellooooo" with trailing `o's) and amplifies character-level features intsead (capitalized first letter, lexical similarity to other known named entity token `Marshmello', etc ), thereby suppressing noise information (“UNK" token embedding) in decoding steps  Note that most of the previous literature in NER or other NLP tasks combine word and character-level information with naive concatenation, which is vulnerable to noisy social media posts  When an auxiliary image is available, the modality attention module determines to amplify this visual context in disambiguating polysemous entities, or to attenuate visual contexts when they are irrelevant to target named entities, selfies, etc  Note that the proposed modality attention module is distinct from how attention is used in other sequence-to-sequence literature (e g  attending to a specific token within an input sequence)  Section SECREF2 provides the detailed literature review 
Our contributions are three-fold: we propose (1) an LSTM-CNN hybrid multimodal NER network that takes as input both image and text for recognition of a named entity in text input  To the best of our knowledge, our approach is the first work to incorporate visual contexts for named entity recognition tasks  (2) We propose a general modality attention module that selectively chooses modalities to extract primary context from, maximizing information gain and suppressing irrelevant contexts from each modality (we treat words, characters, and images as separate modalities)  (3) We show that the proposed approaches outperform the state-of-the-art NER models (both with and without using additional visual contexts) on our new MNER dataset SnapCaptions, a large collection of informal and extremely short social media posts paired with unique images 
Related Work
Neural models for NER have been recently proposed, producing state-of-the-art performance on standard NER tasks  For example, some of the end-to-end NER systems BIBREF4 , BIBREF2 , BIBREF3 , BIBREF0 , BIBREF1 use a recurrent neural network usually with a CRF BIBREF5 , BIBREF6 for sequence labeling, accompanied with feature extractors for words and characters (CNN, LSTMs, etc ), and achieve the state-of-the-art performance mostly without any use of gazetteers information  Note that most of these work aggregate textual contexts via concatenation of word embeddings and character embeddings  Recently, several work have addressed the NER task specifically on noisy short text segments such as Tweets, etc  BIBREF7 , BIBREF8   They report performance gains from leveraging external sources of information such as lexical information (POS tags, etc ) and/or from several preprocessing steps (token substitution, etc )  Our model builds upon these state-of-the-art neural models for NER tasks, and improves the model in two critical ways: (1) incorporation of visual contexts to provide auxiliary information for short media posts, and (2) addition of the modality attention module, which better incorporates word embeddings and character embeddings, especially when there are many missing tokens in the given word embedding matrix  Note that we do not explore the use of gazetteers information or other auxiliary information (POS tags, etc ) BIBREF9 as it is not the focus of our study 
Attention modules are widely applied in several deep learning tasks BIBREF10 , BIBREF11 , BIBREF12 , BIBREF13   For example, they use an attention module to attend to a subset within a single input (a part/region of an image, a specific token in an input sequence of tokens, etc ) at each decoding step in an encoder-decoder framework for image captioning tasks, etc  BIBREF14 explore various attention mechanisms in NLP tasks, but do not incorporate visual components or investigate the impact of such models on noisy social media data  BIBREF15 propose to use attention for a subset of discrete source samples in transfer learning settings  Our modality attention differs from the previous approaches in that we attenuate or amplifies each modality input as a whole among multiple available modalities, and that we use the attention mechanism essentially to map heterogeneous modalities in a single joint embedding space  Our approach also allows for re-use of the same model for predicting labels even when some of the modalities are missing in input, as other modalities would still preserve the same semantics in the embeddings space 
Multimodal learning is studied in various domains and applications, aimed at building a joint model that extracts contextual information from multiple modalities (views) of parallel datasets 
The most relevant task to our multimodal NER system is the task of multimodal machine translation BIBREF16 , BIBREF17 , which aims at building a better machine translation system by taking as input a sentence in a source language as well as a corresponding image  Several standard sequence-to-sequence architectures are explored (a target-language LSTM decoder that takes as input an image first)  Other previous literature include study of Canonical Correlation Analysis (CCA) BIBREF18 to learn feature correlations among multiple modalities, which is widely used in many applications  Other applications include image captioning BIBREF10 , audio-visual recognition BIBREF19 , visual question answering systems BIBREF20 , etc 
To the best of our knowledge, our approach is the first work to incorporate visual contexts for named entity recognition tasks 
Proposed Methods
Figure FIGREF2 illustrates the proposed multimodal NER (MNER) model  First, we obtain word embeddings, character embeddings, and visual features (Section SECREF3 )  A Bi-LSTM-CRF model then takes as input a sequence of tokens, each of which comprises a word token, a character sequence, and an image, in their respective representation (Section SECREF4 )  At each decoding step, representations from each modality are combined via the modality attention module to produce an entity label for each token ( SECREF5 )  We formulate each component of the model in the following subsections 
Notations: Let INLINEFORM0 a sequence of input tokens with length INLINEFORM1 , with a corresponding label sequence INLINEFORM2 indicating named entities (e g  in standard BIO formats)  Each input token is composed of three modalities: INLINEFORM3 for word embeddings, character embeddings, and visual embeddings representations, respectively 
Features
Similar to the state-of-the-art NER approaches BIBREF0 , BIBREF1 , BIBREF8 , BIBREF4 , BIBREF2 , BIBREF3 , we use both word embeddings and character embeddings 
Word embeddings are obtained from an unsupervised learning model that learns co-occurrence statistics of words from a large external corpus, yielding word embeddings as distributional semantics BIBREF21   Specifically, we use pre-trained embeddings from GloVE BIBREF22  
Character embeddings are obtained from a Bi-LSTM which takes as input a sequence of characters of each token, similarly to BIBREF0   An alternative approach for obtaining character embeddings is using a convolutional neural network as in BIBREF1 , but we find that Bi-LSTM representation of characters yields empirically better results in our experiments 
Visual embeddings: To extract features from an image, we take the final hidden layer representation of a modified version of the convolutional network model called Inception (GoogLeNet) BIBREF23 , BIBREF24 trained on the ImageNet dataset BIBREF25 to classify multiple objects in the scene  Our implementation of the Inception model has deep 22 layers, training of which is made possible via “network in network" principles and several dimension reduction techniques to improve computing resource utilization  The final layer representation encodes discriminative information describing what objects are shown in an image, which provide auxiliary contexts for understanding textual tokens and entities in accompanying captions 
Incorporating this visual information onto the traditional NER system is an open challenge, and multiple approaches can be considered  For instance, one may provide visual contexts only as an initial input to decoder as in some encoder-decoder image captioning systems BIBREF26   However, we empirically observe that an NER decoder which takes as input the visual embeddings at every decoding step (Section SECREF4 ), combined with the modality attention module (Section SECREF5 ), yields better results 
Lastly, we add a transform layer for each feature INLINEFORM0 before it is fed to the NER entity LSTM 
Bi-LSTM + CRF for Multimodal NER
Our MNER model is built on a Bi-LSTM and CRF hybrid model  We use the following implementation for the entity Bi-LSTM 
it = (Wxiht-1 + Wcict-1)
ct = (1-it) ct-1
+ it tanh(Wxcxt + Whcht-1)
ot = (Wxoxt + Whoht-1 + Wcoct)
ht = LSTM(xt)
= ot tanh(ct)
where INLINEFORM0 is a weighted average of three modalities INLINEFORM1 via the modality attention module, which will be defined in Section SECREF5   Bias terms for gates are omitted here for simplicity of notation 
We then obtain bi-directional entity token representations INLINEFORM0 by concatenating its left and right context representations  To enforce structural correlations between labels in sequence decoding, INLINEFORM1 is then passed to a conditional random field (CRF) to produce a label for each token maximizing the following objective  y* = y p(y|h; WCRF)
p(y|h; WCRF) = t t (yt-1,yt;h) y' t t (y't-1,y't;h)
where INLINEFORM0 is a potential function, INLINEFORM1 is a set of parameters that defines the potential functions and weight vectors for label pairs ( INLINEFORM2 )  Bias terms are omitted for brevity of formulation 
The model can be trained via log-likelihood maximization for the training set INLINEFORM0 :
L(WCRF) = i p(y|h; W)
Modality Attention
The modality attention module learns a unified representation space for multiple available modalities (words, characters, images, etc ), and produces a single vector representation with aggregated knowledge among multiple modalities, based on their weighted importance  We motivate this module from the following observations 
A majority of the previous literature combine the word and character-level contexts by simply concatenating the word and character embeddings at each decoding step, e g  INLINEFORM0 in Eq  SECREF4   However, this naive concatenation of two modalities (word and characters) results in inaccurate decoding, specifically for unknown word token embeddings (an all-zero vector INLINEFORM1 or a random vector INLINEFORM2 is assigned for any unknown token INLINEFORM3 , thus INLINEFORM4 or INLINEFORM5 )  While this concatenation approach does not cause significant errors for well-formatted text, we observe that it induces performance degradation for our social media post datasets which contain a significant number of missing tokens 
Similarly, naive merging of textual and visual information ( INLINEFORM0 ) yields suboptimal results as each modality is treated equally informative, whereas in our datasets some of the images may contain irrelevant contexts to textual modalities  Hence, ideally there needs a mechanism in which the model can effectively turn the switch on and off the modalities adaptive to each sample 
To this end, we propose a general modality attention module, which adaptively attenuates or emphasizes each modality as a whole at each decoding step INLINEFORM0 , and produces a soft-attended context vector INLINEFORM1 as an input token for the entity LSTM  [at(w),at(c),at(v)] = (Wm[xt(w); xt(c); xt(v)] + bm )
t(m) = (at(m))m'{w,c,v}(at(m')) m {w,c,v}
xt = m{w,c,v} t(m)xt(m)
where INLINEFORM0 is an attention vector at each decoding step INLINEFORM1 , and INLINEFORM2 is a final context vector at INLINEFORM3 that maximizes information gain for INLINEFORM4   Note that the optimization of the objective function (Eq  SECREF4 ) with modality attention (Eq  SECREF5 ) requires each modality to have the same dimension ( INLINEFORM5 ), and that the transformation via INLINEFORM6 essentially enforces each modality to be mapped into the same unified subspace, where the weighted average of which encodes discrimitive features for recognition of named entities 
When visual context is not provided with each token (as in the traditional NER task), we can define the modality attention for word and character embeddings only in a similar way: [at(w),at(c)] = (Wm[xt(w); xt(c)] + bm )
t(m) = (at(m))m'{w,c}(at(m')) m {w,c}
xt = m{w,c} t(m)xt(m)
Note that while we apply this modality attention module to the Bi-LSTM+CRF architecture (Section SECREF4 ) for its empirical superiority, the module itself is flexible and thus can work with other NER architectures or for other multimodal applications 
SnapCaptions Dataset
The SnapCaptions dataset is composed of 10K user-generated image (snap) and textual caption pairs where named entities in captions are manually labeled by expert human annotators (entity types: PER, LOC, ORG, MISC)  These captions are collected exclusively from snaps submitted to public and crowd-sourced stories (aka Snapchat Live Stories or Our Stories)  Examples of such public crowd-sourced stories are “New York Story” or “Thanksgiving Story”, which comprise snaps that are aggregated for various public events, venues, etc  All snaps were posted between year 2016 and 2017, and do not contain raw images or other associated information (only textual captions and obfuscated visual descriptor features extracted from the pre-trained InceptionNet are available)  We split the dataset into train (70%), validation (15%), and test sets (15%)  The captions data have average length of 30 7 characters (5 81 words) with vocabulary size 15,733, where 6,612 are considered unknown tokens from Stanford GloVE embeddings BIBREF22   Named entities annotated in the SnapCaptions dataset include many of new and emerging entities, and they are found in various surface forms (various nicknames, typos, etc ) To the best of our knowledge, SnapCaptions is the only dataset that contains natural image-caption pairs with expert-annotated named entities 
Baselines
Task: given a caption and a paired image (if used), the goal is to label every token in a caption in BIO scheme (B: beginning, I: inside, O: outside) BIBREF27   We report the performance of the following state-of-the-art NER models as baselines, as well as several configurations of our proposed approach to examine contributions of each component (W: word, C: char, V: visual) 
Bi-LSTM/CRF (W only): only takes word token embeddings (Stanford GloVE) as input  The rest of the architecture is kept the same 
Bi-LSTM/CRF + Bi-CharLSTM (C only): only takes a character sequence of each word token as input  (No word embeddings)
Bi-LSTM/CRF + Bi-CharLSTM (W+C) BIBREF0 : takes as input both word embeddings and character embeddings extracted from a Bi-CharLSTM  Entity LSTM takes concatenated vectors of word and character embeddings as input tokens 
Bi-LSTM/CRF + CharCNN (W+C) BIBREF1 : uses character embeddings extracted from a CNN instead 
Bi-LSTM/CRF + CharCNN (W+C) + Multi-task BIBREF8 : trains the model to perform both recognition (into multiple entity types) as well as segmentation (binary) tasks 
(proposed) Bi-LSTM/CRF + Bi-CharLSTM with modality attention (W+C): uses the modality attention to merge word and character embeddings 
(proposed) Bi-LSTM/CRF + Bi-CharLSTM + Inception (W+C+V): takes as input visual contexts extracted from InceptionNet as well, concatenated with word and char vectors 
(proposed) Bi-LSTM/CRF + Bi-CharLSTM + Inception with modality attention (W+C+V): uses the modality attention to merge word, character, and visual embeddings as input to entity LSTM 
Results: SnapCaptions Dataset
Table TABREF6 shows the NER performance on the Snap Captions dataset  We report both entity types recognition (PER, LOC, ORG, MISC) and named entity segmentation (named entity or not) results 
Parameters: We tune the parameters of each model with the following search space (bold indicate the choice for our final model): character embeddings dimension: {25, 50, 100, 150, 200, 300}, word embeddings size: {25, 50, 100, 150, 200, 300}, LSTM hidden states: {25, 50, 100, 150, 200, 300}, and INLINEFORM0 dimension: {25, 50, 100, 150, 200, 300}  We optimize the parameters with Adagrad BIBREF28 with batch size 10, learning rate 0 02, epsilon INLINEFORM1 , and decay 0 0 
Main Results: When visual context is available (W+C+V), we see that the model performance greatly improves over the textual models (W+C), showing that visual contexts are complimentary to textual information in named entity recognition tasks  In addition, it can be seen that the modality attention module further improves the entity type recognition performance for (W+C+V)  This result indicates that the modality attention is able to focus on the most effective modality (visual, words, or characters) adaptive to each sample to maximize information gain  Note that our text-only model (W+C) with the modality attention module also significantly outperform the state-of-the-art baselines BIBREF8 , BIBREF1 , BIBREF0 that use the same textual modalities (W+C), showing the effectiveness of the modality attention module for textual models as well 
Error Analysis: Table TABREF17 shows example cases where incorporation of visual contexts affects prediction of named entities  For example, the token `curry' in the caption “The curry's " is polysemous and may refer to either a type of food or a famous basketball player `Stephen Curry', and the surrounding textual contexts do not provide enough information to disambiguate it  On the other hand, visual contexts (visual tags: `parade', `urban area',    ) provide similarities to the token's distributional semantics from other training examples (snaps from “NBA Championship Parade Story"), and thus the model successfully predicts the token as a named entity  Similarly, while the text-only model erroneously predicts `Apple' in the caption “Grandma w dat lit Apple Crisp" as an organization (Apple Inc ), the visual contexts (describing objects related to food) help disambiguate the token, making the model predict it correctly as a non-named entity (a fruit)  Trending entities (musicians or DJs such as `CID', `Duke Dumont', `Marshmello', etc ) are also recognized correctly with strengthened contexts from visual information (describing concert scenes) despite lack of surrounding textual contexts  A few cases where visual contexts harmed the performance mostly include visual tags that are unrelated to a token or its surrounding textual contexts 
Visualization of Modality Attention: Figure FIGREF19 visualizes the modality attention module at each decoding step (each column), where amplified modality is represented with darker color, and attenuated modality is represented with lighter color 
For the image-aided model (W+C+V; upper row in Figure FIGREF19 ), we confirm that the modality attention successfully attenuates irrelevant signals (selfies, etc ) and amplifies relevant modality-based contexts in prediction of a given token  In the example of “disney word essential = coffee" with visual tags selfie, phone, person, the modality attention successfully attenuates distracting visual signals and focuses on textual modalities, consequently making correct predictions  The named entities in the examples of “Beautiful night atop The Space Needle" and “Splash Mountain" are challenging to predict because they are composed of common nouns (space, needle, splash, mountain), and thus they often need additional contexts to correctly predict  In the training data, visual contexts make stronger indicators for these named entities (space needle, splash mountain), and the modality attention module successfully attends more to stronger signals 
For text-only model (W+C), we observe that performance gains mostly come from the modality attention module better handling tokens unseen during training or unknown tokens from the pre-trained word embeddings matrix  For example, while WaRriOoOrs and Kooler Matic are missing tokens in the word embeddings matrix, it successfully amplifies character-based contexts (capitalized first letters, similarity to known entities `Golden State Warriors') and suppresses word-based contexts (word embeddings for unknown tokens `WaRriOoOrs'), leading to correct predictions  This result is significant because it shows performance of the model, with an almost identical architecture, can still improve without having to scale the word embeddings matrix indefinitely 
Figure FIGREF19 (b) shows the cases where the modality attention led to incorrect predictions  For example, the model predicts missing tokens HUUUGE and Shampooer incorrectly as named entities by amplifying misleading character-based contexts (capitalized first letters) or visual contexts (concert scenes, associated contexts of which often include named entities in the training dataset) 
Sensitivity to Word Embeddings Vocabulary Size: In order to isolate the effectiveness of the modality attention module on textual models in handling missing tokens, we report the performance with varying word embeddings vocabulary sizes in Table TABREF20   By increasing the number of missing tokens artificially by randomly removing words from the word embeddings matrix (original vocab size: 400K), we observe that while the overall performance degrades, the modality attention module is able to suppress the peformance degradation  Note also that the performance gap generally gets bigger as we decrease the vocabulary size of the word embeddings matrix  This result is significant in that the modality attention is able to improve the model more robust to missing tokens without having to train an indefinitely large word embeddings matrix for arbitrarily noisy social media text datasets 
Conclusions
We proposed a new multimodal NER (MNER: image + text) task on short social media posts  We demonstrated for the first time an effective MNER system, where visual information is combined with textual information to outperform traditional text-based NER baselines  Our work can be applied to myriads of social media posts or other articles across multiple platforms which often include both text and accompanying images  In addition, we proposed the modality attention module, a new neural mechanism which learns optimal integration of different modes of correlated information  In essence, the modality attention learns to attenuate irrelevant or uninformative modal information while amplifying the primary modality to extract better overall representations  We showed that the modality attention based model outperforms other state-of-the-art baselines when text was the only modality available, by better combining word and character level information 
Context 3: Introduction
Measures of semantic similarity and relatedness quantify the degree to which two concepts are similar (e g , INLINEFORM0 – INLINEFORM1 ) or related (e g , INLINEFORM2 – INLINEFORM3 )  Semantic similarity can be viewed as a special case of semantic relatedness – to be similar is one of many ways that a pair of concepts may be related  The automated discovery of groups of semantically similar or related terms is critical to improving the retrieval BIBREF0 and clustering BIBREF1 of biomedical and clinical documents, and the development of biomedical terminologies and ontologies BIBREF2  
There is a long history in using distributional methods to discover semantic similarity and relatedness (e g , BIBREF3 , BIBREF4 , BIBREF5 , BIBREF6 )  These methods are all based on the distributional hypothesis, which holds that two terms that are distributionally similar (i e , used in the same context) will also be semantically similar BIBREF7 , BIBREF8   Recently word embedding techniques such as word2vec BIBREF9 have become very popular  Despite the prominent role that neural networks play in many of these approaches, at their core they remain distributional techniques that typically start with a word by word co–occurrence matrix, much like many of the more traditional approaches 
However, despite these successes distributional methods do not perform well when data is very sparse (which is common)  One possible solution is to use second–order co–occurrence vectors BIBREF10 , BIBREF11   In this approach the similarity between two words is not strictly based on their co–occurrence frequencies, but rather on the frequencies of the other words which occur with both of them (i e , second order co–occurrences)  This approach has been shown to be successful in quantifying semantic relatedness BIBREF12 , BIBREF13   However, while more robust in the face of sparsity, second–order methods can result in significant amounts of noise, where contextual information that is overly general is included and does not contribute to quantifying the semantic relatedness between the two concepts 
Our goal then is to discover methods that automatically reduce the amount of noise in a second–order co–occurrence vector  We achieve this by incorporating pairwise semantic similarity scores derived from a taxonomy into our second–order vectors, and then using these scores to select only the most semantically similar co–occurrences (thereby reducing noise) 
We evaluate our method on two datasets that have been annotated in multiple ways  One has been annotated for both similarity and relatedness, and the other has been annotated for relatedness by two different types of experts (medical doctors and medical coders)  Our results show that integrating second order co–occurrences with measures of semantic similarity increases correlation with our human reference standards  We also compare our result to a number of other studies which have applied various word embedding methods to the same reference standards we have used  We find that our method often performs at a comparable or higher level than these approaches  These results suggest that our methods of integrating semantic similarity and relatedness values have the potential to improve performance of purely distributional methods 
Similarity and Relatedness Measures
This section describes the similarity and relatedness measures we integrate in our second–order co–occurrence vectors  We use two taxonomies in this study, SNOMED–CT and MeSH  SNOMED–CT (Systematized Nomenclature of Medicine Clinical Terms) is a comprehensive clinical terminology created for the electronic representation of clinical health information  MeSH (Medical Subject Headings) is a taxonomy of biomedical terms developed for indexing biomedical journal articles 
We obtain SNOMED–CT and MeSH via the Unified Medical Language System (UMLS) Metathesaurus (version 2016AA)  The Metathesaurus contains approximately 2 million biomedical and clinical concepts from over 150 different terminologies that have been semi–automatically integrated into a single source  Concepts in the Metathesaurus are connected largely by two types of hierarchical relations: INLINEFORM0 / INLINEFORM1 (PAR/CHD) and INLINEFORM2 / INLINEFORM3 (RB/RN) 
Similarity Measures
Measures of semantic similarity can be classified into three broad categories : path–based, feature–based and information content (IC)  Path–based similarity measures use the structure of a taxonomy to measure similarity – concepts positioned close to each other are more similar than those further apart  Feature–based methods rely on set theoretic measures of overlap between features (union and intersection)  The information content measures quantify the amount of information that a concept provides – more specific concepts have a higher amount of information content 
RadaMBB89 introduce the Conceptual Distance measure  This measure is simply the length of the shortest path between two concepts ( INLINEFORM0 and INLINEFORM1 ) in the MeSH hierarchy  Paths are based on broader than (RB) and narrower than (RN) relations  CaviedesC04 extends this measure to use parent (PAR) and child (CHD) relations  Our INLINEFORM2 measure is simply the reciprocal of this shortest path value (Equation EQREF3 ), so that larger values (approaching 1) indicate a high degree of similarity  DISPLAYFORM0
While the simplicity of INLINEFORM0 is appealing, it can be misleading when concepts are at different levels of specificity  Two very general concepts may have the same path length as two very specific concepts  WuP94 introduce a correction to INLINEFORM1 that incorporates the depth of the concepts, and the depth of their Least Common Subsumer (LCS)  This is the most specific ancestor two concepts share  In this measure, similarity is twice the depth of the two concept's LCS divided by the product of the depths of the individual concepts (Equation EQREF4 )  Note that if there are multiple LCSs for a pair of concepts, the deepest of them is used in this measure  DISPLAYFORM0
ZhongZLY02 take a very similar approach and again scale the depth of the LCS by the sum of the depths of the two concepts (Equation EQREF5 ), where INLINEFORM0   The value of INLINEFORM1 was set to 2 based on their recommendations  DISPLAYFORM0
PekarS02 offer another variation on INLINEFORM0 , where the shortest path of the two concepts to the LCS is used, in addition to the shortest bath between the LCS and the root of the taxonomy (Equation EQREF6 )  DISPLAYFORM0
Feature–based methods represent each concept as a set of features and then measure the overlap or sharing of features to measure similarity  In particular, each concept is represented as the set of their ancestors, and similarity is a ratio of the intersection and union of these features 
MaedcheS01 quantify the similarity between two concepts as the ratio of the intersection over their union as shown in Equation EQREF8   DISPLAYFORM0
BatetSV11 extend this by excluding any shared features (in the numerator) as shown in Equation EQREF9   DISPLAYFORM0
Information content is formally defined as the negative log of the probability of a concept  The effect of this is to assign rare (low probability) concepts a high measure of information content, since the underlying assumption is that more specific concepts are less frequently used than more common ones 
Resnik95 modified this notion of information content in order to use it as a similarity measure  He defines the similarity of two concepts to be the information content of their LCS (Equation EQREF11 )  DISPLAYFORM0
JiangC97, Lin98, and PirroE10 extend INLINEFORM0 by incorporating the information content of the individual concepts in various different ways  Lin98 defines the similarity between two concepts as the ratio of information content of the LCS with the sum of the individual concept's information content (Equation EQREF12 )  Note that INLINEFORM1 has the same form as INLINEFORM2 and INLINEFORM3 , and is in effect using information content as a measure of specificity (rather than depth)  If there is more than one possible LCS, the LCS with the greatest IC is chosen  DISPLAYFORM0
JiangC97 define the distance between two concepts to be the sum of the information content of the two concepts minus twice the information content of the concepts' LCS  We modify this from a distance to a similarity measure by taking the reciprocal of the distance (Equation EQREF13 )  Note that the denominator of INLINEFORM0 is very similar to the numerator of INLINEFORM1   DISPLAYFORM0
PirroE10 define the similarity between two concepts as the information content of the two concept's LCS divided by the sum of their individual information content values minus the information content of their LCS (Equation EQREF14 )  Note that INLINEFORM0 can be viewed as a set–theoretic version of INLINEFORM1   DISPLAYFORM0
Information Content
The information content of a concept may be derived from a corpus (corpus–based) or directly from a taxonomy (intrinsic–based)  In this work we focus on corpus–based techniques 
For corpus–based information content, we estimate the probability of a concept INLINEFORM0 by taking the sum of the probability of the concept INLINEFORM1 and the probability its descendants INLINEFORM2 (Equation EQREF16 )  DISPLAYFORM0
The initial probabilities of a concept ( INLINEFORM0 ) and its descendants ( INLINEFORM1 ) are obtained by dividing the number of times each concept and descendant occurs in the corpus, and dividing that by the total numbers of concepts ( INLINEFORM2 ) 
Ideally the corpus from which we are estimating the probabilities of concepts will be sense–tagged  However, sense–tagging is a challenging problem in its own right, and it is not always possible to carry out reliably on larger amounts of text  In fact in this paper we did not use any sense–tagging of the corpus we derived information content from 
Instead, we estimated the probability of a concept by using the UMLSonMedline dataset  This was created by the National Library of Medicine and consists of concepts from the 2009AB UMLS and the counts of the number of times they occurred in a snapshot of Medline taken on 12 January, 2009  These counts were obtained by using the Essie Search Engine BIBREF14 which queried Medline with normalized strings from the 2009AB MRCONSO table in the UMLS  The frequency of a CUI was obtained by aggregating the frequency counts of the terms associated with the CUI to provide a rough estimate of its frequency  The information content measures then use this information to calculate the probability of a concept 
Another alternative is the use of Intrinsic Information Content  It assess the informativeness of concept based on its placement within a taxonomy by considering the number of incoming (ancestors) relative to outgoing (descendant) links BIBREF15 (Equation EQREF17 )  DISPLAYFORM0
where INLINEFORM0 are the number of descendants of concept INLINEFORM1 that are leaf nodes, INLINEFORM2 are the number of concept INLINEFORM3 's ancestors and INLINEFORM4 are the total number of leaf nodes in the taxonomy 
Relatedness Measures
Lesk86 observed that concepts that are related should share more words in their respective definitions than concepts that are less connected  He was able to perform word sense disambiguation by identifying the senses of words in a sentence with the largest number of overlaps between their definitions  An overlap is the longest sequence of one or more consecutive words that occur in both definitions  BanerjeeP03 extended this idea to WordNet, but observed that WordNet glosses are often very short, and did not contain enough information to distinguish between multiple concepts  Therefore, they created a super–gloss for each concept by adding the glosses of related concepts to the gloss of the concept itself (and then finding overlaps) 
PatwardhanP06 adapted this measure to second–order co–occurrence vectors  In this approach, a vector is created for each word in a concept's definition that shows which words co–occur with it in a corpus  These word vectors are averaged to create a single co-occurrence vector for the concept  The similarity between the concepts is calculated by taking the cosine between the concepts second–order vectors  LiuMPMP12 modified and extended this measure to be used to quantify the relatedness between biomedical and clinical terms in the UMLS  The work in this paper can be seen as a further extension of PatwardhanP06 and LiuMPMP12 
Method
In this section, we describe our second–order similarity vector measure  This incorporates both contextual information using the term pair's definition and their pairwise semantic similarity scores derived from a taxonomy  There are two stages to our approach  First, a co–occurrence matrix must be constructed  Second, this matrix is used to construct a second–order co–occurrence vector for each concept in a pair of concepts to be measured for relatedness 
Co–occurrence Matrix Construction
We build an INLINEFORM0 similarity matrix using an external corpus where the rows and columns represent words within the corpus and the element contains the similarity score between the row word and column word using the similarity measures discussed above  If a word maps to more than one possible sense, we use the sense that returns the highest similarity score

ground_truth: Yes

Yes

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

ground_truth: 0.5115

0.6103

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 embedding techniques are explored in the paper?
Context 3: 
For this paper our external corpus was the NLM 2015 Medline baseline  Medline is a bibliographic database containing over 23 million citations to journal articles in the biomedical domain and is maintained by National Library of Medicine  The 2015 Medline Baseline encompasses approximately 5,600 journals starting from 1948 and contains 23,343,329 citations, of which 2,579,239 contain abstracts  In this work, we use Medline titles and abstracts from 1975 to present day  Prior to 1975, only 2% of the citations contained an abstract  We then calculate the similarity for each bigram in this dataset and include those that have a similarity score greater than a specified threshold on these experiments 
Measure Term Pairs for Relatedness
We obtain definitions for each of the two terms we wish to measure  Due to the sparsity and inconsistencies of the definitions in the UMLS, we not only use the definition of the term (CUI) but also include the definition of its related concepts  This follows the method proposed by PatwardhanP06 for general English and WordNet, and which was adapted for the UMLS and the medical domain by LiuMPMP12  In particular we add the definitions of any concepts connected via a parent (PAR), child (CHD), RB (broader than), RN (narrower than) or TERM (terms associated with CUI) relation  All of the definitions for a term are combined into a single super–gloss  At the end of this process we should have two super–glosses, one for each term to be measured for relatedness 
Next, we process each super–gloss as follows:
We extract a first–order co–occurrence vector for each term in the super–gloss from the co–occurrence matrix created previously 
We take the average of the first order co–occurrence vectors associated with the terms in a super–gloss and use that to represent the meaning of the term  This is a second–order co–occurrence vector 
After a second–order co–occurrence vector has been constructed for each term, then we calculate the cosine between these two vectors to measure the relatedness of the terms 
Data
We use two reference standards to evaluate the semantic similarity and relatedness measures   UMNSRS was annotated for both similarity and relatedness by medical residents  MiniMayoSRS was annotated for relatedness by medical doctors (MD) and medical coders (coder)  In this section, we describe these data sets and describe a few of their differences 
MiniMayoSRS: The MayoSRS, developed by PakhomovPMMRC10, consists of 101 clinical term pairs whose relatedness was determined by nine medical coders and three physicians from the Mayo Clinic  The relatedness of each term pair was assessed based on a four point scale: (4 0) practically synonymous, (3 0) related, (2 0) marginally related and (1 0) unrelated  MiniMayoSRS is a subset of the MayoSRS and consists of 30 term pairs on which a higher inter–annotator agreement was achieved  The average correlation between physicians is 0 68  The average correlation between medical coders is 0 78  We evaluate our method on the mean of the physician scores, and the mean of the coders scores in this subset in the same manner as reported by PedersenPPC07 
UMNSRS: The University of Minnesota Semantic Relatedness Set (UMNSRS) was developed by PakhomovMALPM10, and consists of 725 clinical term pairs whose semantic similarity and relatedness was determined independently by four medical residents from the University of Minnesota Medical School  The similarity and relatedness of each term pair was annotated based on a continuous scale by having the resident touch a bar on a touch sensitive computer screen to indicate the degree of similarity or relatedness  The Intraclass Correlation Coefficient (ICC) for the reference standard tagged for similarity was 0 47, and 0 50 for relatedness  Therefore, as suggested by Pakhomov and colleagues,we use a subset of the ratings consisting of 401 pairs for the similarity set and 430 pairs for the relatedness set which each have an ICC of 0 73 
Experimental Framework
We conducted our experiments using the freely available open source software package UMLS::Similarity BIBREF16 version 1 47  This package takes as input two terms (or UMLS concepts) and returns their similarity or relatedness using the measures discussed in Section SECREF2  
Correlation between the similarity measures and human judgments were estimated using Spearman's Rank Correlation ( INLINEFORM0 )  Spearman's measures the statistical dependence between two variables to assess how well the relationship between the rankings of the variables can be described using a monotonic function  We used Fisher's r-to-z transformation BIBREF17 to calculate the significance between the correlation results 
Results and Discussion
Table TABREF26 shows the Spearman's Rank Correlation between the human scores from the four reference standards and the scores from the various measures of similarity introduced in Section SECREF2   Each class of measure is followed by the scores obtained when integrating our second order vector approach with these measures of semantic similarity 
Results Comparison
The results for UMNSRS tagged for similarity ( INLINEFORM0 ) and MiniMayoSRS tagged by coders show that all of the second-order similarity vector measures ( INLINEFORM1 ) except for INLINEFORM2 - INLINEFORM3 obtain a higher correlation than the original measures  We found that INLINEFORM4 - INLINEFORM5 and INLINEFORM6 - INLINEFORM7 obtain the highest correlations of all these results with human judgments 
For the UMNSRS dataset tagged for relatedness and MiniMayoSRS tagged by physicians (MD), the original INLINEFORM0 measure obtains a higher correlation than our measure ( INLINEFORM1 ) although the difference is not statistically significant ( INLINEFORM2 ) 
In order to analyze and better understand these results, we filtered the bigram pairs used to create the initial similarity matrix based on the strength of their similarity using the INLINEFORM0 and the INLINEFORM1 measures  Note that the INLINEFORM2 measure holds to a 0 to 1 scale, while INLINEFORM3 ranges from 0 to an unspecified upper bound that is dependent on the size of the corpus from which information content is estimated  As such we use a different range of threshold values for each measure  We discuss the results of this filtering below 
Thresholding Experiments
Table TABREF29 shows the results of applying the threshold parameter on each of the reference standards using the INLINEFORM0 measure  For example, a threshold of 0 indicates that all of the bigrams were included in the similarity matrix; and a threshold of 1 indicates that only the bigram pairs with a similarity score greater than one were included 
These results show that using a threshold cutoff of 2 obtains the highest correlation for the UMNSRS dataset, and that a threshold cutoff of 4 obtains the highest correlation for the MiniMayoSRS dataset  All of the results show an increase in correlation with human judgments when incorporating a threshold cutoff over all of the original measures  The increase in the correlation for the UMNSRS tagged for similarity is statistically significant ( INLINEFORM0 ), however this is not the case for the UMNSRS tagged for relatedness nor for the MiniMayoSRS data 
Similarly, Table TABREF30 shows the results of applying the threshold parameter (T) on each of the reference standards using the INLINEFORM0 measure  Although, unlike INLINEFORM1 whose scores are greater than or equal to 0 without an upper limit, the INLINEFORM2 measure returns scores between 0 and 1 (inclusive)  Therefore, here a threshold of 0 indicates that all of the bigrams were included in the similarity matrix; and a threshold of INLINEFORM3 indicates that only the bigram pairs with a similarity score greater than INLINEFORM4 were included  The results show an increase in accuracy for all of the datasets except for the MiniMayoSRS tagged for physicians  The increase in the results for the UMNSRS tagged for similarity and the MayoSRS is statistically significant ( INLINEFORM5 )  This is not the case for the UMNSRS tagged for relatedness nor the MiniMayoSRS 
Overall, these results indicate that including only those bigrams that have a sufficiently high similarity score increases the correlation results with human judgments, but what quantifies as sufficiently high varies depending on the dataset and measure 
Comparison with Previous Work
Recently, word embeddings BIBREF9 have become a popular method for measuring semantic relatedness in the biomedical domain  This is a neural network based approach that learns a representation of a word by word co–occurrence matrix  The basic idea is that the neural network learns a series of weights (the hidden layer within the neural network) that either maximizes the probability of a word given its context, referred to as the continuous bag of words (CBOW) approach, or that maximizes the probability of the context given a word, referred to as the Skip–gram approach  These approaches have been used in numerous recent papers 
muneeb2015evalutating trained both the Skip–gram and CBOW models over the PubMed Central Open Access (PMC) corpus of approximately 1 25 million articles  They evaluated the models on a subset of the UMNSRS data, removing word pairs that did not occur in their training corpus more than ten times  chiu2016how evaluated both the the Skip–gram and CBOW models over the PMC corpus and PubMed  They also evaluated the models on a subset of the UMNSRS ignoring those words that did not appear in their training corpus  Pakhomov2016corpus trained CBOW model over three different types of corpora: clinical (clinical notes from the Fairview Health System), biomedical (PMC corpus), and general English (Wikipedia)  They evaluated their method using a subset of the UMNSRS restricting to single word term pairs and removing those not found within their training corpus  sajad2015domain trained the Skip–gram model over CUIs identified by MetaMap on the OHSUMED corpus, a collection of 348,566 biomedical research articles  They evaluated the method on the complete UMNSRS, MiniMayoSRS and the MayoSRS datasets; any subset information about the dataset was not explicitly stated therefore we believe a direct comparison may be possible 
In addition, a previous work very closely related to ours is a retrofitting vector method proposed by YuCBJW16 that incorporates ontological information into a vector representation by including semantically related words  In their measure, they first map a biomedical term to MeSH terms, and second build a word vector based on the documents assigned to the respective MeSH term  They then retrofit the vector by including semantically related words found in the Unified Medical Language System  They evaluate their method on the MiniMayoSRS dataset 
Table TABREF31 shows a comparison to the top correlation scores reported by each of these works on the respective datasets (or subsets) they evaluated their methods on  N refers to the number of term pairs in the dataset the authors report they evaluated their method  The table also includes our top scoring results: the integrated vector-res and vector-faith  The results show that integrating semantic similarity measures into second–order co–occurrence vectors obtains a higher or on–par correlation with human judgments as the previous works reported results with the exception of the UMNSRS rel dataset  The results reported by Pakhomov2016corpus and chiu2016how obtain a higher correlation although the results can not be directly compared because both works used different subsets of the term pairs from the UMNSRS dataset 
Conclusion and Future Work
We have presented a method for quantifying the similarity and relatedness between two terms that integrates pair–wise similarity scores into second–order vectors  The goal of this approach is two–fold  First, we restrict the context used by the vector measure to words that exist in the biomedical domain, and second, we apply larger weights to those word pairs that are more similar to each other  Our hypothesis was that this combination would reduce the amount of noise in the vectors and therefore increase their correlation with human judgments  We evaluated our method on datasets that have been manually annotated for relatedness and similarity and found evidence to support this hypothesis  In particular we discovered that guiding the creation of a second–order context vector by selecting term pairs from biomedical text based on their semantic similarity led to improved levels of correlation with human judgment 
We also explored using a threshold cutoff to include only those term pairs that obtained a sufficiently large level of similarity  We found that eliminating less similar pairs improved the overall results (to a point)  In the future, we plan to explore metrics to automatically determine the threshold cutoff appropriate for a given dataset and measure  We also plan to explore additional features that can be integrated with a second–order vector measure that will reduce the noise but still provide sufficient information to quantify relatedness  We are particularly interested in approaches that learn word, phrase, and sentence embeddings from structured corpora such as literature BIBREF23 and dictionary entries BIBREF24   Such embeddings could be integrated into a second–order vector or be used on their own 
Finally, we compared our proposed method to other distributional approaches, focusing on those that used word embeddings  Our results showed that integrating semantic similarity measures into second–order co–occurrence vectors obtains the same or higher correlation with human judgments as do various different word embedding approaches  However, a direct comparison was not possible due to variations in the subsets of the UMNSRS evaluation dataset used  In the future, we would not only like to conduct a direct comparison but also explore integrating semantic similarity into various kinds of word embeddings by training on pair–wise values of semantic similarity as well as co–occurrence statistics 

ground_truth: Skip–gram, CBOW

integrated vector-res, vector-faith, Skip–gram, CBOW