Timely and accurate extraction of Adverse Drug Events (ADE) from biomedical literature is paramount for public safety, but involves slow and costly manual labor. We set out to improve drug safety monitoring (pharmacovigilance, PV) through the use of Natural Language Processing (NLP). We introduce BioDEX, a large-scale resource for Biomedical adverse Drug Event eXtraction, rooted in the historical output of drug safety reporting in the U.S. BioDEX consists of 65k abstracts and 19k full-text biomedical papers with 256k associated document-level safety reports created by medical experts. The core features of these reports include the reported weight, age, and biological sex of a patient, a set of drugs taken by the patient, the drug dosages, the reactions experienced, and whether the reaction was life threatening. In this work, we consider the task of predicting the core information of the report given its originating paper. We estimate human performance to be 72.0% F1, whereas our best model achieves 59.1% F1 (62.3 validation), indicating significant headroom. We also begin to explore ways in which these models could help professional PV reviewers. Our code and data are available at https://github.com/KarelDO/BioDEX.

This paper shines a light on the potential of definition-based semantic models for detecting idiomatic and semi-idiomatic multiword expressions (MWEs) in clinical terminology. Our study focuses on biomedical entities defined in the UMLS ontology and aims to help prioritize the translation efforts of these entities. In particular, we develop an effective tool for scoring the idiomaticity of biomedical MWEs based on the degree of similarity between the semantic representations of those MWEs and a weighted average of the representation of their constituents. We achieve this using a biomedical language model trained to produce similar representations for entity names and their definitions, called BioLORD. The importance of this definition-based approach is highlighted by comparing the BioLORD model to two other state-of-the-art biomedical language models based on Transformer: SapBERT and CODER. Our results show that the BioLORD model has a strong ability to identify idiomatic MWEs, not replicated in other models. Our corpus-free idiomaticity estimation helps ontology translators to focus on more challenging MWEs.

Question Generation (QG) systems have shown promising results in reducing the time and effort required to create questions for students. Typically, a first step in QG is to select the content to design a question for. In an educational setting, it is crucial that the resulting questions cover the most relevant/important pieces of knowledge the student should have acquired. Yet, current QG systems either consider just a single sentence or paragraph (thus do not include a selection step), or do not consider this educational viewpoint of content selection. Aiming to fill this research gap with a solution for educational document level QG, we thus propose to select contents for QG based on relevance and topic diversity. We demonstrate the effectiveness of our proposed content selection strategy for QG on 2 educational datasets. In our performance assessment, we also highlight limitations of existing QG evaluation metrics in light of the content selection problem.

Intent discovery is the task of inferring latent intents from a set of unlabeled utterances, and is a useful step towards the efficient creation of new conversational agents. We show that recent competitive methods in intent discovery can be outperformed by clustering utterances based on abstractive summaries, i.e., “labels”, that retain the core elements while removing non-essential information. We contribute the IDAS approach, which collects a set of descriptive utterance labels by prompting a Large Language Model, starting from a well-chosen seed set of prototypical utterances, to bootstrap an In-Context Learning procedure to generate labels for non-prototypical utterances. The utterances and their resulting noisy labels are then encoded by a frozen pre-trained encoder, and subsequently clustered to recover the latent intents. For the unsupervised task (without any intent labels) IDAS outperforms the state-of-the-art by up to +7.42% in standard cluster metrics for the Banking, StackOverflow, and Transport datasets. For the semi-supervised task (with labels for a subset of intents) IDAS surpasses 2 recent methods on the CLINC benchmark without even using labeled data.

Background: More than 400.000 biomedical concepts and some of their relationships are contained in SnomedCT, a comprehensive biomedical ontology. However, their concept names are not always readily interpretable by non-experts, or patients looking at their own electronic health records (EHR). Clear definitions or descriptions in understandable language or often not available. Therefore, generating human-readable definitions for biomedical concepts might help make the information they encode more accessible and understandable to a wider public. Objective: In this article, we introduce the Automatic Glossary of Clinical Terminology (AGCT), a large-scale biomedical dictionary of clinical concepts generated using high-quality information extracted from the biomedical knowledge contained in SnomedCT.Methods: We generate a novel definition for every SnomedCT concept, after prompting the OpenAI Turbo model, a variant of GPT 3.5, using a high-quality verbalization of the SnomedCT relationships of the to-be-defined concept. A significant subset of the generated definitions was subsequently evaluated by NLP researchers with biomedical expertise on 5-point scales along the following three axes: factuality, insight, and fluency. Results: AGCT contains 422,070 computer-generated definitions for SnomedCT concepts, covering various domains such as diseases, procedures, drugs, and anatomy. The average length of the definitions is 49 words. The definitions were assigned average scores of over 4.5 out of 5 on all three axes, indicating a majority of factual, insightful, and fluent definitions. Conclusion: AGCT is a novel and valuable resource for biomedical tasks that require human-readable definitions for SnomedCT concepts. It can also serve as a base for developing robust biomedical retrieval models or other applications that leverage natural language understanding of biomedical knowledge.

Since performing exercises (including, e.g.,practice tests) forms a crucial component oflearning, and creating such exercises requiresnon-trivial effort from the teacher. There is agreat value in automatic exercise generationin digital tools in education. In this paper, weparticularly focus on automatic creation of gap-filling exercises for language learning, specifi-cally grammar exercises. Since providing anyannotation in this domain requires human ex-pert effort, we aim to avoid it entirely and ex-plore the task of converting existing texts intonew gap-filling exercises, purely based on anexample exercise, without explicit instructionor detailed annotation of the intended gram-mar topics. We contribute (i) a novel neuralnetwork architecture specifically designed foraforementioned gap-filling exercise generationtask, and (ii) a real-world benchmark datasetfor French grammar. We show that our modelfor this French grammar gap-filling exercisegeneration outperforms a competitive baselineclassifier by 8% in F1 percentage points, achiev-ing an average F1 score of 82%. Our model im-plementation and the dataset are made publiclyavailable to foster future research, thus offeringa standardized evaluation and baseline solutionof the proposed partially annotated data predic-tion task in grammar exercise creation.

In this paper, we present ECL, a novel multimodal dataset containing the textual and numerical data from corporate 10K filings and associated binary bankruptcy labels. Furthermore, we develop and critically evaluate several classical and neural bankruptcy prediction models using this dataset. Our findings suggest that the information contained in each data modality is complementary for bankruptcy prediction. We also see that the binary bankruptcy prediction target does not enable our models to distinguish next year bankruptcy from an unhealthy financial situation resulting in bankruptcy in later years. Finally, we explore the use of LLMs in the context of our task. We show how GPT-based models can be used to extract meaningful summaries from the textual data but zero-shot bankruptcy prediction results are poor. All resources required to access and update the dataset or replicate our experiments are available on github.com/henriarnoUG/ECL.

This work introduces BioLORD, a new pre-training strategy for producing meaningful representations for clinical sentences and biomedical concepts. State-of-the-art methodologies operate by maximizing the similarity in representation of names referring to the same concept, and preventing collapse through contrastive learning. However, because biomedical names are not always self-explanatory, it sometimes results in non-semantic representations. BioLORD overcomes this issue by grounding its concept representations using definitions, as well as short descriptions derived from a multi-relational knowledge graph consisting of biomedical ontologies. Thanks to this grounding, our model produces more semantic concept representations that match more closely the hierarchical structure of ontologies. BioLORD establishes a new state of the art for text similarity on both clinical sentences (MedSTS) and biomedical concepts (MayoSRS).

This pilot study employs the Wizard of Oz technique to collect a corpus of written human-computer conversations in the domain of customer service. The resulting dataset contains 192 conversations and is used to test three hypotheses related to the expression and annotation of emotions. First, we hypothesize that there is a discrepancy between the emotion annotations of the participant (the experiencer) and the annotations of our external annotator (the observer). Furthermore, we hypothesize that the personality of the participants has an influence on the emotions they expressed, and on the way they evaluated (annotated) these emotions. We found that for an external, trained annotator, not all emotion labels were equally easy to work with. We also noticed that the trained annotator had a tendency to opt for emotion labels that were more centered in the valence-arousal space, while participants made more ‘extreme’ annotations. For the second hypothesis, we discovered a positive correlation between the personality trait extraversion and the emotion dimensions valence and dominance in our sample. Finally, for the third premise, we observed a positive correlation between the internal-external agreement on emotion labels and the personality traits conscientiousness and extraversion. Our insights and findings will be used in future research to conduct a larger Wizard of Oz experiment.

The ability to track fine-grained emotions in customer service dialogues has many real-world applications, but has not been studied extensively. This paper measures the potential of prediction models on that task, based on a real-world dataset of Dutch Twitter conversations in the domain of customer service. We find that modeling emotion trajectories has a small, but measurable benefit compared to predictions based on isolated turns. The models used in our study are shown to generalize well to different companies and economic sectors.

We consider the task of document-level entity linking (EL), where it is important to make consistent decisions for entity mentions over the full document jointly. We aim to leverage explicit “connections” among mentions within the document itself: we propose to join EL and coreference resolution (coref) in a single structured prediction task over directed trees and use a globally normalized model to solve it. This contrasts with related works where two separate models are trained for each of the tasks and additional logic is required to merge the outputs. Experimental results on two datasets show a boost of up to +5% F1-score on both coref and EL tasks, compared to their standalone counterparts. For a subset of hard cases, with individual mentions lacking the correct EL in their candidate entity list, we obtain a +50% increase in accuracy.

Models for bankruptcy prediction are useful in several real-world scenarios, and multiple research contributions have been devoted to the task, based on structured (numerical) as well as unstructured (textual) data. However, the lack of a common benchmark dataset and evaluation strategy impedes the objective comparison between models. This paper introduces such a benchmark for the unstructured data scenario, based on novel and established datasets, in order to stimulate further research into the task. We describe and evaluate several classical and neural baseline models, and discuss benefits and flaws of different strategies. In particular, we find that a lightweight bag-of-words model based on static in-domain word representations obtains surprisingly good results, especially when taking textual data from several years into account. These results are critically assessed, and discussed in light of particular aspects of the data and the task. All code to replicate the data and experimental results will be released.

This work presents the contribution from the Text-to-Knowledge team of Ghent University (UGent-T2K) to the MultiDoc2Dial shared task on modeling dialogs grounded in multiple documents. We propose a pipeline system, comprising (1) document retrieval, (2) passage retrieval, and (3) response generation. We engineered these individual components mainly by, for (1)-(2), combining multiple ranking models and adding a final LambdaMART reranker, and, for (3), by adopting a Fusion-in-Decoder (FiD) model. We thus significantly boost the baseline system’s performance (over +10 points for both F1 and SacreBLEU). Further, error analysis reveals two major failure cases, to be addressed in future work: (i) in case of topic shift within the dialog, retrieval often fails to select the correct grounding document(s), and (ii) generation sometimes fails to use the correctly retrieved grounding passage. Our code is released at this link.

For text classification tasks, finetuned language models perform remarkably well. Yet, they tend to rely on spurious patterns in training data, thus limiting their performance on out-of-distribution (OOD) test data. Among recent models aiming to avoid this spurious pattern problem, adding extra counterfactual samples to the training data has proven to be very effective. Yet, counterfactual data generation is costly since it relies on human annotation. Thus, we propose a novel solution that only requires annotation of a small fraction (e.g., 1%) of the original training data, and uses automatic generation of extra counterfactuals in an encoding vector space. We demonstrate the effectiveness of our approach in sentiment classification, using IMDb data for training and other sets for OOD tests (i.e., Amazon, SemEval and Yelp). We achieve noticeable accuracy improvements by adding only 1% manual counterfactuals: +3% compared to adding +100% in-distribution training samples, +1.3% compared to alternate counterfactual approaches.

Powerful sentence encoders trained for multiple languages are on the rise. These systems are capable of embedding a wide range of linguistic properties into vector representations. While explicit probing tasks can be used to verify the presence of specific linguistic properties, it is unclear whether the vector representations can be manipulated to indirectly steer such properties. For efficient learning, we investigate the use of a geometric mapping in embedding space to transform linguistic properties, without any tuning of the pre-trained sentence encoder or decoder. We validate our approach on three linguistic properties using a pre-trained multilingual autoencoder and analyze the results in both monolingual and cross-lingual settings.

In online domain-specific customer service applications, many companies struggle to deploy advanced NLP models successfully, due to the limited availability of and noise in their datasets. While prior research demonstrated the potential of migrating large open-domain pretrained models for domain-specific tasks, the appropriate (pre)training strategies have not yet been rigorously evaluated in such social media customer service settings, especially under multilingual conditions. We address this gap by collecting a multilingual social media corpus containing customer service conversations (865k tweets), comparing various pipelines of pretraining and finetuning approaches, applying them on 5 different end tasks. We show that pretraining a generic multilingual transformer model on our in-domain dataset, before finetuning on specific end tasks, consistently boosts performance, especially in non-English settings.

Large annotated corpora for coreference resolution are available for few languages. For machine translation, however, strong black-box systems exist for many languages. We empirically explore the appealing idea of leveraging such translation tools for bootstrapping coreference resolution in languages with limited resources. Two scenarios are analyzed, in which a large coreference corpus in a high-resource language is used for coreference predictions in a smaller language, i.e., by machine translating either the training corpus or the test data. In our empirical evaluation of coreference resolution using the two scenarios on several medium-resource languages, we find no improvement over monolingual baseline models. Our analysis of the various sources of error inherent to the studied scenarios, reveals that in fact the quality of contemporary machine translation tools is the main limiting factor.

We propose a newly annotated dataset for information extraction on recipes. Unlike previous approaches to machine comprehension of procedural texts, we avoid a priori pre-defining domain-specific predicates to recognize (e.g., the primitive instructionsin MILK) and focus on basic understanding of the expressed semantics rather than directly reduce them to a simplified state representation (e.g., ProPara). We thus frame the semantic comprehension of procedural text such as recipes, as fairly generic NLP subtasks, covering (i) entity recognition (ingredients, tools and actions), (ii) relation extraction (what ingredients and tools are involved in the actions), and (iii) zero anaphora resolution (link actions to implicit arguments, e.g., results from previous recipe steps). Further, our Recipe Instruction Semantic Corpus (RISeC) dataset includes textual descriptions for the zero anaphora, to facilitate language generation thereof. Besides the dataset itself, we contribute a pipeline neural architecture that addresses entity and relation extractionas well an identification of zero anaphora. These basic building blocks can facilitate more advanced downstream applications (e.g., question answering, conversational agents).

This paper introduces improved methods for sub-event detection in social media streams, by applying neural sequence models not only on the level of individual posts, but also directly on the stream level. Current approaches to identify sub-events within a given event, such as a goal during a soccer match, essentially do not exploit the sequential nature of social media streams. We address this shortcoming by framing the sub-event detection problem in social media streams as a sequence labeling task and adopt a neural sequence architecture that explicitly accounts for the chronological order of posts. Specifically, we (i) establish a neural baseline that outperforms a graph-based state-of-the-art method for binary sub-event detection (2.7% micro-F1 improvement), as well as (ii) demonstrate superiority of a recurrent neural network model on the posts sequence level for labeled sub-events (2.4% bin-level F1 improvement over non-sequential models).

This paper describes IDLab’s text classification systems submitted to Task A as part of the CLPsych 2019 shared task. The aim of this shared task was to develop automated systems that predict the degree of suicide risk of people based on their posts on Reddit. Bag-of-words features, emotion features and post level predictions are used to derive user-level predictions. Linear models and ensembles of these models are used to predict final scores. We find that predicting fine-grained risk levels is much more difficult than flagging potentially at-risk users. Furthermore, we do not find clear added value from building richer ensembles compared to simple baselines, given the available training data and the nature of the prediction task.

Short text clustering is a challenging problem when adopting traditional bag-of-words or TF-IDF representations, since these lead to sparse vector representations of the short texts. Low-dimensional continuous representations or embeddings can counter that sparseness problem: their high representational power is exploited in deep clustering algorithms. While deep clustering has been studied extensively in computer vision, relatively little work has focused on NLP. The method we propose, learns discriminative features from both an autoencoder and a sentence embedding, then uses assignments from a clustering algorithm as supervision to update weights of the encoder network. Experiments on three short text datasets empirically validate the effectiveness of our method.

Inducing sparseness while training neural networks has been shown to yield models with a lower memory footprint but similar effectiveness to dense models. However, sparseness is typically induced starting from a dense model, and thus this advantage does not hold during training. We propose techniques to enforce sparseness upfront in recurrent sequence models for NLP applications, to also benefit training. First, in language modeling, we show how to increase hidden state sizes in recurrent layers without increasing the number of parameters, leading to more expressive models. Second, for sequence labeling, we show that word embeddings with predefined sparseness lead to similar performance as dense embeddings, at a fraction of the number of trainable parameters.

This paper describes the IDLab system submitted to Task A of the CLPsych 2018 shared task. The goal of this task is predicting psychological health of children based on language used in hand-written essays and socio-demographic control variables. Our entry uses word- and character-based features as well as lexicon-based features and features derived from the essays such as the quality of the language. We apply linear models, gradient boosting as well as neural-network based regressors (feed-forward, CNNs and RNNs) to predict scores. We then make ensembles of our best performing models using a weighted average.

Adversarial training (AT) is a regularization method that can be used to improve the robustness of neural network methods by adding small perturbations in the training data. We show how to use AT for the tasks of entity recognition and relation extraction. In particular, we demonstrate that applying AT to a general purpose baseline model for jointly extracting entities and relations, allows improving the state-of-the-art effectiveness on several datasets in different contexts (i.e., news, biomedical, and real estate data) and for different languages (English and Dutch).

Character-level features are currently used in different neural network-based natural language processing algorithms. However, little is known about the character-level patterns those models learn. Moreover, models are often compared only quantitatively while a qualitative analysis is missing. In this paper, we investigate which character-level patterns neural networks learn and if those patterns coincide with manually-defined word segmentations and annotations. To that end, we extend the contextual decomposition technique (Murdoch et al. 2018) to convolutional neural networks which allows us to compare convolutional neural networks and bidirectional long short-term memory networks. We evaluate and compare these models for the task of morphological tagging on three morphologically different languages and show that these models implicitly discover understandable linguistic rules.

Many Machine Reading and Natural Language Understanding tasks require reading supporting text in order to answer questions. For example, in Question Answering, the supporting text can be newswire or Wikipedia articles; in Natural Language Inference, premises can be seen as the supporting text and hypotheses as questions. Providing a set of useful primitives operating in a single framework of related tasks would allow for expressive modelling, and easier model comparison and replication. To that end, we present Jack the Reader (JACK), a framework for Machine Reading that allows for quick model prototyping by component reuse, evaluation of new models on existing datasets as well as integrating new datasets and applying them on a growing set of implemented baseline models. JACK is currently supporting (but not limited to) three tasks: Question Answering, Natural Language Inference, and Link Prediction. It is developed with the aim of increasing research efficiency and code reuse.

Comprehending lyrics, as found in songs and poems, can pose a challenge to human and machine readers alike. This motivates the need for systems that can understand the ambiguity and jargon found in such creative texts, and provide commentary to aid readers in reaching the correct interpretation. We introduce the task of automated lyric annotation (ALA). Like text simplification, a goal of ALA is to rephrase the original text in a more easily understandable manner. However, in ALA the system must often include additional information to clarify niche terminology and abstract concepts. To stimulate research on this task, we release a large collection of crowdsourced annotations for song lyrics. We analyze the performance of translation and retrieval models on this task, measuring performance with both automated and human evaluation. We find that each model captures a unique type of information important to the task.

In this paper, we address the (to the best of our knowledge) new problem of extracting a structured description of real estate properties from their natural language descriptions in classifieds. We survey and present several models to (a) identify important entities of a property (e.g.,rooms) from classifieds and (b) structure them into a tree format, with the entities as nodes and edges representing a part-of relation. Experiments show that a graph-based system deriving the tree from an initially fully connected entity graph, outperforms a transition-based system starting from only the entity nodes, since it better reconstructs the tree.