Croatia

The number of scientific publications in the biomedical domain is continuously increasing with time. An efficient system for indexing these publications is required to make the information accessible according to the user’s information needs. Task 10a of the BioASQ challenge aims to classify PubMed articles according to the MeSH ontology so that new publications can be grouped with similar preexisting publications in the field without the assistance of time-consuming and costly annotations by human annotators. In this work, we use Graph Neural Network (GNN) in the link prediction setting to exploit potential graph-structured information present in the dataset which could otherwise be neglected by transformer-based models. Additionally, we provide error analysis and a plausible reason for the substandard performance achieved by GNN.

EACL 2023

Annotating PubMed Abstracts with MeSH Headings using Graph Neural Network

bioasq challenge

negative sampling

link prediction

graph neural network

workshop paper

### Welcome to the 17th Conference of the European Chapter of the Association for Computational Linguistics (EACL) 
Continuing its mission of expanding and involving the science community of all European countries, EACL had selected the Ukrainian community for the 16th EACL, which took place online due to the COVID pandemic. Unfortunately, the ongoing war made the organisation in Kyiv impossible. Considering the importance of physical interaction among researchers, especially after the restrictions imposed by the COVID pandemic, in addition to an online mode, the conference will be held in Dubrovnik, Croatia, from 2 to 6 of May, 2023. The original aim of strengthening the connection with the Ukrainian community will not change as our program will feature a dedicated session and a workshop to highlight work on Ukrainian language technologies. As the flagship European conference in the field of computational linguistics, EACL welcomes European and international researchers covering a broad spectrum of research areas that are concerned with computational approaches to natural language.

You need to register for the conference in order to access this site. Please visit https://2023.eacl.org/registration for more information.

As the flagship European conference in the field of computational linguistics, EACL welcomes European and international researchers covering a broad spectrum of research areas that are concerned with computational approaches to natural language.

Demographic factors (e.g., gender or age) shape our language. Previous work showed that incorporating demographic factors can consistently improve performance for various NLP tasks with traditional NLP models. In this work, we investigate whether these previous findings still hold with state-of-the-art pretrained Transformer-based language models (PLMs). We use three common specialization methods proven effective for incorporating external knowledge into pretrained Transformers (e.g., domain-specific or geographic knowledge). We adapt the language representations for the demographic dimensions of gender and age, using continuous language modeling and dynamic multi-task learning for adaptation, where we couple language modeling objectives with the prediction of demographic classes. Our results, when employing a multilingual PLM, show substantial gains in task performance across four languages (English, German, French, and Danish), which is consistent with the results of previous work. However, controlling for confounding factors - primarily domain and language proficiency of Transformer-based PLMs -- shows that downstream performance gains from our demographic adaptation do not actually stem from demographic knowledge. Our results indicate that demographic specialization of PLMs, while holding promise for positive societal impact, still represents an unsolved problem for (modern) NLP.

Can Demographic Factors Improve Text Classification? Revisiting Demographic Adaptation in the Age of Transformers

Active learning has been widely used in the task of text classification for its ability to select the most valuable samples to annotate while improving the model performance. However, the efficiency of active learning in multi-label text classification tasks has been under-explored due to the label imbalanceness problem. In this paper, we conduct an empirical study of active learning on multi-label text classification and evaluate the efficiency of five active learning strategies on six multi-label text classification tasks. The experiments show some strategies in the single-label setting especially in imbalanced datasets.

An Empirical Study on Active Learning for Multi-label Text Classification

Low-quality data can cause downstream problems in high-stakes applications. Data-centric approach emphasizes on improving dataset quality to enhance model performance. High-quality datasets are needed for general-purpose Large Language Models (LLMs) training, as well as for domain-specific models, which are usually small in size as it is costly to engage a large number of domain experts for their creation. Thus, it is vital to ensure high-quality domain-specific training data. In this paper, we propose a framework for enhancing the data quality of original datasets. We applied the proposed framework to four biomedical datasets and showed relative improvement of up to 33%/40% for fine-tuning of retrieval/reader models on the BioASQ dataset when using back translation to enhance the original dataset quality.

A Data-centric Framework for Improving Domain-specific Machine Reading Comprehension Datasets

In recent years, there has been growing interest in the field of abstractive text summarization with focused contributions in relevant model architectures, datasets, and evaluation metrics. Despite notable research advances, previous works have identified certain limitations concerning the quality of datasets and the effectiveness
of evaluation techniques for generated summaries. In this context, we examine these
limitations further with the help of three quality measures, namely, Information Coverage, Entity Hallucination, and Summarization Complexity. As a part of this work, we investigate two widely used datasets (XSUM and CNNDM) and three existing models (BART, PEGASUS, and BRIO) and report our findings. Some key insights are: 1) Cumulative ROUGE score is an inappropriate evaluation measure since few high-scoring samples dominate the overall performance, 2) Existing summarization models have limited capability for information coverage and hallucinate to generate factual information, and 3) Compared to the model-generated summaries, the reference summaries have lowest information coverage and highest entity hallucinations reiterating the need of new and better reference summaries.

Hiding in Plain Sight: Insights into Abstractive Text Summarization

Context-aware translation can be achieved by processing a concatenation of consecutive sentences with the standard Transformer architecture.
This paper investigates the intuitive idea of providing the model with explicit information about the position of the sentences contained in the concatenation window.
We compare various methods to encode sentence positions into token representations, including novel methods. Our results show that the Transformer benefits from certain sentence position encoding methods on En-Ru, if trained with a context-discounted loss (Lupo et al., 2022). However, the same benefits are not observed on En-De. Further empirical efforts are necessary to define the conditions under which the proposed approach is beneficial.

Encoding Sentence Position in Context-Aware Neural Machine Translation with Concatenation

Recent research has demonstrated impressive generalization capabilities of several Knowledge Base Question Answering (KBQA) models on the GrailQA dataset. We inspect whether these models can generalize to other datasets in a zero-shot setting. We notice a significant drop in performance and investigate the causes for the same. We observe that the models are dependent not only on the structural complexity of the questions, but also on the linguistic styles of framing a question. Specifically, the linguistic dimensions corresponding to explicitness, readability, coherence, and grammaticality have a significant impact on the performance of state-of-the-art KBQA models. Overall our results showcase the brittleness of such models and the need for creating generalizable systems.

Exploring the Reasons for Non-generalizability of KBQA systems

Entities and events are crucial to natural language reasoning and common in procedural texts. Existing work has focused either exclusively on entity state tracking (e.g., whether a pan is hot) or on event reasoning (e.g., whether one would burn themselves by touching the pan), while these two tasks are often causally related. We propose CREPE, the first benchmark on causal reasoning of event plausibility and entity states. We show that most language models, including GPT-3, perform close to chance at .35 F1, lagging far behind human at .87 F1. We boost model performance to .59 F1 by creatively representing events as programming languages while prompting language models pretrained on code. By injecting the causal relations between entities and events as intermediate reasoning steps in our representation, we further boost the performance to .67 F1. Our findings indicate not only the challenge that CREPE brings for language models, but also the efficacy of code-like prompting combined with chain-of-thought prompting for multihop event reasoning.

Causal Reasoning About Entities and Events in Procedural Texts

Given a sentence "Abby told Brittney that she upset Courtney", one would struggle to understand who "she" refers to, and ask for clarification. However, if the word "upset" were replaced with "hugged", "she" unambiguously refers to Abby. We study if modern coreference resolution models are sensitive to such pronominal ambiguity. To this end, we construct AmbiCoref, a diagnostic corpus of minimal sentence pairs with ambiguous and unambiguous referents. Our examples generalize psycholinguistic studies of human perception of ambiguity around particular arrangements of verbs and their arguments. Analysis shows that (1) humans are less sure of referents in ambiguous AmbiCoref examples than unambiguous ones, and (2) most coreference models show little difference in output between ambiguous and unambiguous pairs. We release AmbiCoref as a diagnostic corpus for testing whether models treat ambiguity similarly to humans.

AMBICOREF: Evaluating Human and Model Sensitivity to Ambiguous Coreference

In this paper, we evaluate a fine-tuned BERT model’s performance on a set of auxiliary probe tasks to gauge whether the model can indirectly encode discourse properties. The focus is on structural properties that have proven important predictors in feature-based Event Coreference Resolution (ECR). We demonstrate that fine-tuning a language model for ECR also increases performance for event prominence and sentiment matching tasks. This contradicts earlier work where coreference models seemed unable to encode any sort of significant structural or discourse information.

What Does BERT actually Learn about Event Coreference? Probing Structural Information in a Fine-Tuned Dutch Language Model

Recent works on tokenizer-free multilingual pretrained models show promising results in improving cross-lingual transfer and reducing engineering overhead compared to subword-based alternatives. However, previous work mainly focuses on reporting accuracy on a limited set of tasks and data settings, placing less emphasis on other important factors when tuning and deploying the models in practice, such as memory usage, inference speed, and fine-tuning data efficiency. We attempt to fill this gap by performing a comprehensive empirical comparison of multilingual tokenizer-free and subword-based models considering the various dimensions. Surprisingly, we find that subword-based models might still be the most practical choice in many settings, achieving better performance for lower inference latency and memory usage. Based on these results, we encourage future work in tokenizer-free methods to consider these factors when designing and evaluating new models.

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Annotating PubMed Abstracts with MeSH Headings using Graph Neural Network

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Can Demographic Factors Improve Text Classification? Revisiting Demographic Adaptation in the Age of Transformers

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