United Arab Emirates

This work presents a two-stage approach for tackling low-resource AMR-to-text generation for Brazilian Portuguese. Our approach consists of (1) generating a masked surface realization in which some tokens are masked according to its Part-of-Speech class and (2) infilling the masked tokens according to the AMR graph and the previous masked surface realization. Results show a slight improvement over the baseline, mainly in BLEU (1.63) and METEOR (0.02) scores. Moreover, we evaluate the pipeline components separately, showing that the bottleneck of the pipeline is the masked surface realization. Finally, the human evaluation suggests that models still suffer from hallucinations, and some strategies to deal with the problems found are proposed.

EMNLP 2022

Exploring a POS-based Two-stage Approach for Improving Low-Resource AMR-to-Text Generation

pipeline approach

low-resource nlg

amr-to-text generation

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The great event is jointly organized by the Association for Computational Linguistics (ACL) and Asian Federation of Natural Language Processing (AFNLP).

workshop paper

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Expressing natural language descriptions of structured facts or relations -- data-to-text generation (D2T) -- increases the accessibility of structured knowledge repositories. Previous work shows that pre-trained language models (PLMs) perform remarkably well on this task after fine-tuning on a significant amount of task-specific training data. On the other hand, while auto-regressive PLMs can generalize from a few task examples, their efficacy at D2T is largely unexplored. Furthermore, we have an incomplete understanding of the limits of PLMs on D2T. In this work, we conduct an empirical study of both fine-tuned and auto-regressive PLMs on the DART multi-domain D2T dataset. We consider their performance as a function of the amount of task-specific data and how the data is incorporated into the models: zero and few-shot learning, and fine-tuning of model weights. In addition, we probe the limits of PLMs by measuring performance on subsets of the evaluation data: novel predicates and abstractive test examples. To improve the performance on these subsets, we investigate two techniques: providing predicate descriptions in the context and re-ranking generated candidates by information reflected in the source. Finally, we conduct a human evaluation of model errors and show that D2T generation tasks would benefit from datasets with more careful manual curation.

What Makes Data-to-Text Generation Hard for Pretrained Language Models?

In the medical field, we have seen the emergence of health-bots that interact with patients to gather data and track their state. One of the downstream application is automatic questionnaire filling, where the content of the dialog is used to automatically fill a pre-defined medical questionnaire. Previous work has shown that answering questions from the dialog context can successfully be cast as a Natural Language Inference (NLI) task and therefore benefit from current pre-trained NLI models. However, NLI models have mostly been trained on text rather than dialogs, which may have an influence on their performance. In this paper, we study the influence of content transformation and content selection on the questionnaire filling task. Our results demonstrate that dialog pre-processing can significantly improve the performance of zero-shot questionnaire filling models which take health-bots dialogs as input.

Exploring the Influence of Dialog Input Format for Unsupervised Clinical Questionnaire Filling

Nested Named Entity Recognition (NER) is an information extraction task that aims to identify entities that may be nested within other entity mentions. Despite the availability of several corpora with nested entities in the Spanish clinical domain, most previous work has overlooked them due to the lack of models and a clear annotation scheme for dealing with the task. To fill this gap, this paper provides an empirical study of straightforward methods for tackling the nested NER task on two Spanish clinical datasets, Clinical Trials, and the Chilean Waiting List. We assess the advantages and limitations of two sequence labeling approaches; one based on Multiple LSTM-CRF architectures and another on Joint labeling models. To better understand the differences between these models, we compute task-specific metrics that adequately measure the ability of models to detect nested entities and perform a fine-grained comparison across models. Our experimental results show that employing domain-specific language models trained from scratch significantly improves the performance obtained with strong domain-specific and general-domain baselines, achieving state-of-the-art results in both datasets. Specifically, we obtained F1 scores of 89.21 and 83.16 in Clinical Trials and the Chilean Waiting List, respectively. Interestingly enough, we observe that the task-specific metrics and analysis properly reflect the limitations of the models when recognizing nested entities. Finally, we perform a case study on an aggregated NER dataset created from several clinical corpora in Spanish. We highlight how entity length and the simultaneous recognition of inner and outer entities are the most critical variables for the nested NER task.

Assessing the Limits of Straightforward Models for Nested Named Entity Recognition in Spanish Clinical Narratives

The medical codes prediction problem from clinical notes has received substantial interest in the NLP community, and several recent studies have shown the state-of-the-art (SOTA) code prediction results of full-fledged deep learning-based methods. However, most previous SOTA works based on deep learning are still in early stages in terms of providing textual references and explanations of the predicted codes, despite the fact that this level of explainability of the prediction outcomes is critical to gaining trust from professional medical coders. This raises the important question of how well current explainability methods apply to advanced neural network models such as transformers to predict correct codes and present references in clinical notes that support code prediction. First, we present an explainable Read, Attend, and Code (xRAC) framework and assess two approaches, attention score-based xRAC-ATTN and model-agnostic knowledge-distillation-based xRAC-KD, through simplified but thorough human-grounded evaluations with SOTA transformer-based model, RAC. We find that the supporting evidence text highlighted by xRAC-ATTN is of higher quality than xRAC-KD whereas xRAC-KD has potential advantages in production deployment scenarios. More importantly, we show for the first time that, given the current state of explainability methodologies, using the SOTA medical codes prediction system still requires the expertise and competencies of professional coders, even though its prediction accuracy is superior to that of human coders. This, we believe, is a very meaningful step toward developing explainable and accurate machine learning systems for fully autonomous medical code prediction from clinical notes.

Can Current Explainability Help Provide References in Clinical Notes to Support Humans Annotate Medical Codes?

Scientific documents typically contain numerous entity mentions, while only a subset are directly relevant to the key contributions of the paper. Distinguishing these focus entities from background ones effectively could improve the recovery of relevant documents and the extraction of information from documents. To study the identification of focus entities, we developed two large datasets of disease-causing biological pathogens using MEDLINE, the largest collection of biomedical citations, and PubMed Central, a collection of full text articles. The focus entities were identified using human-curated indexing on these collections. Experiments with machine learning methods to identify focus entities show that transformer methods achieve high precision and recall and that document discourse information is relevant. The work lays the foundation for more targeted retrieval/summarisation of entity-relevant documents.

Distinguishing between focus and background entities in biomedical corpora using discourse structure and transformers

This paper introduces FrenchMedMCQA, the first publicly  available Multiple-Choice Question Answering (MCQA) dataset in French for medical domain. It is composed of 3,105 questions taken from real exams of the French medical specialization diploma in pharmacy, mixing single and multiple answers. Each instance of the dataset contains an identifier, a question, five possible answers and their manual correction(s). We also propose first baseline models to automatically process this MCQA task in order to report on the current performances and to highlight the difficulty of the task. A detailed analysis of the results showed that it is necessary to have representations adapted to the medical domain or to the MCQA task: in our case, English specialized models yielded better results than generic French ones, even though FrenchMedMCQA is in French. Corpus, models and tools are available online.

FrenchMedMCQA: A French Multiple-Choice Question Answering Dataset for Medical domain

Keyphrase generation is the task consisting in generating a set of words or phrases that highlight the main topics of a document. There are few datasets for keyphrase generation in the biomedical domain and they do not meet the expectations in terms of size for training generative models. In this paper, we introduce kp-biomed, the first large-scale biomedical keyphrase generation dataset collected from PubMed abstracts. We train and release several generative models and conduct a series of experiments showing that using large scale datasets improves significantly the performances for present and absent keyphrase generation. The dataset and models are available online.

A Large-Scale Dataset for Biomedical Keyphrase Generation

Clinical notes are the backbone of electronic health records, often containing vital information not observed in other structured data. Unfortunately, the unstructured nature of clinical notes can lead to critical patient-related information being lost. Algorithms that organize clinical notes into distinct sections are often proposed in order to allow medical professionals to better access information in a given note. These algorithms, however, often assume a given partition over the note, and classify section types given this information. In this paper, we propose a multi-task solution for note sectioning, where a single model identifies context changes and labels each section with its medically-relevant title. Results on in-distribution (MIMIC-III) and out-of-distribution (private held-out) datasets reveal that our approach successfully identifies note sections across different hospital systems.

Section Classification in Clinical Notes with Multi-task Transformers

Clinical notes often contain useful information not documented in structured data, but their unstructured nature can lead to critical patient-related information being missed. To increase the likelihood that this valuable information is utilized for patient care, algorithms that summarize notes into a problem list have been proposed. Focused on identifying medically-relevant entities in the free-form text, these solutions are often detached from a canonical ontology and do not allow downstream use of the detected text-spans. Mitigating these issues, we present here a system for generating a canonical problem list from medical notes, consisting of two major stages. At the first stage, annotation, we use a transformer model to detect all clinical conditions which are mentioned in a single note. These clinical conditions are then grounded to a predefined ontology, and are linked to spans in the text. At the second stage, summarization, we develop a novel algorithm that aggregates over the set of clinical conditions detected on all of the patient's notes, and produce a concise patient summary that organizes their most important conditions.

Building a Clinically-Focused Problem List From Medical Notes

Domain adaptation of word embeddings has mainly been  explored in the context of retraining general models on large specialized corpora. While this usually yields good results, we argue that knowledge graphs, which are used less frequently, could also be utilized to enhance existing representations with specialized knowledge. In this work, we aim to shed some light on whether such knowledge injection could be achieved using a basic set of tools: graph-level embeddings and concatenation. To that end, we adopt an incremental approach where we first demonstrate that static embeddings can indeed be improved through concatenation with in-domain node2vec representations. Then, we validate this approach on contextual models and generalize it further by proposing a variant of BERT that incorporates knowledge embeddings within its hidden states through the same process of concatenation. We show that this variant outperforms plain retraining on several specialized tasks, then discuss how this simple approach could be improved further. Both our code and pre-trained models are open-sourced for future research. In this work, we conduct experiments that target the medical domain and the English language.

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