Ireland

Antibiotic resistance has become a growing worldwide concern as new resistance mechanisms are emerging and spreading globally, and thus detecting and collecting the cause – Antibiotic Resistance Genes (ARGs), have been more critical than ever. In this work, we aim to automate the curation of ARGs by extracting ARG-related assertive statements from scientific papers. To support the research towards this direction, we build SCIARG, a new benchmark dataset containing 2,000 manually annotated statements as the evaluation set and 12,516 silver-standard training statements that are automatically created from scientific papers by a set of rules. To set up the baseline performance on SCIARG, we exploit three state-of-the-art neural architectures based on pre-trained language models and prompt tuning, and further ensemble them to attain the highest 77.0% F-score. To the best of our knowledge, we are the first to leverage natural language processing techniques to curate all validated ARGs from scientific papers. Both the code and data are publicly available at https://github.com/VT-NLP/SciARG

ACL 2022

Towards Automatic Curation of Antibiotic Resistance Genes via Statement Extraction from Scientific Papers: A Benchmark Dataset and Models

text classification model design

benchmark sciarg dataset

arg mining

# Welcome everyone to ACL 2022!

The 60th Annual Meeting of the Association for Computational Linguistics is taking place May 22-27, 2022 as a hybrid event, in Dublin and online. We are happy to welcome all of you to this anniversary edition with an almost 50-50 in-person and virtual participation. 
The main conference program features oral presentations, in-person and virtual posters and demo sessions, a plenary session for our best paper presentations and awards, three amazing keynote events and two new initiatives of invited talks: Spotlight Talks for Young Rising Stars (STIRS) and The Next Big Idea Talks. Posters (including Findings of ACL 2022) and demos are grouped by areas for both the in-person and the virtual sessions. For the virtual component, the talks will be on Zoom and the posters and the demos will be in GatherTown. The Student Research Workshop will have an oral session and a poster session as part of Poster Session 1. The program also features eight Tutorials and 28 Workshops. 

 
We wish you a wonderful conference! 
[**The ACL 2022 Organizing Committee**](https://www.2022.aclweb.org/organisers)
 
[**Conference Handbook**](https://drive.google.com/file/d/1_BUCMfhMVrjG9E2e71aHdHeE28KSje0l/view?usp=sharing) 
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The Association for Computational Linguistics (ACL) is the premier international scientific and professional society for people working on computational problems involving human language, a field often referred to as either computational linguistics or natural language processing (NLP). 

workshop paper

It is commonly claimed that inter-annotator agreement (IAA) is the ceiling of machine learning (ML) performance, i.e., that the agreement between an ML system’s predictions and an annotator can not be higher than the agreement between two annotators. Although Boguslav and Cohen (2017) showed that this claim is falsified by many real-world ML systems, the claim has persisted. As a complement to this real-world evidence, we conducted a comprehensive set of simulations, and show that an ML model can outperform IAA even if (and especially if) annotators are noisy and differ in their underlying classification functions, as long as the ML model is reasonably well-specified. Although the latter condition has long been elusive, leading ML models to underperform IAA, we anticipate that this condition will be increasingly met in the era of big data and deep learning. Our work has implications for (1) maximizing the value of machine learning, (2) adherence to ethical standards in computing, and (3) economical use of annotated resources, which is paramount in settings where annotation is especially expensive, like biomedical natural language processing.

Inter-annotator agreement is not the ceiling of machine learning performance: Evidence from a comprehensive set of simulations

Machine learning models that offer excellent predictive performance often lack the interpretability necessary to support integrated human machine decision-making. In clinical medicine and other high-risk settings, domain experts may be unwilling to trust model predictions without explanations. Work in explainable AI must balance competing objectives along two different axes: 1) Models should ideally be both accurate and simple. 2) Explanations must balance faithfulness to the model's decision-making with their plausibility to a domain expert. We propose to use knowledge distillation, or training a student model that mimics the behavior of a trained teacher model, as a technique to generate faithful and plausible explanations. We evaluate our approach on the task of assigning ICD codes to clinical notes to demonstrate that the student model is faithful to the teacher model's behavior and produces quality natural language explanations.

Model Distillation for Faithful Explanations of Medical Code Predictions


Recognizing causal precedence relations among the chemical interactions in biomedical literature is crucial to understanding the underlying biological mechanisms. 
However, detecting such causal relation can be hard because: 
(1) many times, such causal relations among events are not explicitly expressed by certain phrases but implicitly implied by very diverse expressions in the text, and (2) annotating such causal relation detection datasets requires considerable expert knowledge and effort.
In this paper, we propose a strategy to address both challenges by training neural models with in-domain pre-training and knowledge distillation. We show that, by using very limited amount of labeled data, and sufficient amount of unlabeled data, the neural models outperform previous baselines on the causal precedence detection task, and are ten times faster at inference compared to the BERT base model.


Low Resource Causal Event Detection from Biomedical Literature

This paper proposes novel drug-protein relation extraction models that indirectly utilize distant supervision data. Concretely, instead of adding distant supervision data to the manually annotated training data, our models incorporate distantly supervised models that are relation extraction models trained with distant supervision data. Distantly supervised learning has been proposed to generate a large amount of pseudo-training data at low cost. However, there is still a problem of low prediction performance due to the inclusion of mislabeled data. Therefore, several methods have been proposed to suppress the effects of noisy cases by utilizing some manually annotated training data. However, their performance is lower than that of supervised learning on manually annotated data because mislabeled data that cannot be fully suppressed becomes noise when training the model. To overcome this issue, our methods indirectly utilize distant supervision data with manually annotated training data. The experimental results on the DrugProt corpus in the BioCreative VII Track 1 showed that our proposed model can consistently improve the supervised models in different settings.

Improving Supervised Drug-Protein Relation Extraction with Distantly Supervised Models

Cancer immunology research involves several important cell and protein factors. Extracting the information of such cells and proteins and the interactions between them from text are crucial in text mining for cancer immunology research. However, there are few available datasets for these entities, and the amount of annotated documents is not sufficient compared with other major named entity types. In this work, we introduce our automatically annotated dataset of key named entities, i.e., T-cells, cytokines, and transcription factors, which engages the recent cancer immunotherapy. The entities are annotated based on the UniProtKB knowledge base using dictionary matching. We build a neural named entity recognition (NER) model to be trained on this dataset and evaluate it on a manually-annotated data. Experimental results show that we can achieve a promising NER performance even though our data is automatically annotated. Our dataset also enhances the NER performance when combined with existing data, especially gaining improvement in yet investigated named entities such as cytokines and transcription factors.

Named Entity Recognition for Cancer Immunology Research Using Distant Supervision

In this presentation, we propose the two-stage method with cross-modal fusion using the pre-trained language model. We report the performance of our model compared with baselines on the test set in monomodal and multimodal settings. The experimental results show that our method obtains the best performance on the seen test set and unseen official test set, which proves that our method is effective. Finally, we ranked the Top-1 in this shared task 1 of the BioNLP.


VPAI Lab at MedVidQA 2022: A Two Stage Cross-modal Fusion Method for Medical Instructional Video Classification

In this paper, we present an overview of the MedVidQA 2022 shared task, collocated with the 21st BioNLP workshop at ACL 2022. The shared task addressed two of the challenges faced by medical video question answering: (i) a video classification task that explores new approaches to medical video understanding (labeling), and (ii) a visual answer localization task. Visual answer localization refers to the identification of the relevant temporal segments (start and end timestamps) in the video where the answer to the medical question is being shown or illustrated. A total of thirteen teams participated in the shared task challenges, with eleven system descriptions submitted to the workshop. The descriptions present monomodal and multi-modal approaches developed for medical video classification and visual answer localization. This paper describes the tasks, the datasets, evaluation metrics, and baseline systems for both tasks. Finally, the paper summarizes the techniques and results of the evaluation of the various approaches explored by the participating teams.

Overview of the MedVidQA 2022 Shared Task on Medical Video Question-Answering

Algorithmic oppression is an urgent and persistent problem in speech and language technologies. Considering power relations embedded in datasets before compiling or using them to train or test speech and language technologies is essential to designing less harmful, more just technologies. This paper presents a reflective exercise to recognise and challenge gaps and the power relations they reveal in speech and language datasets by applying principles of Data Feminism and Design Justice, and building on work on dataset documentation and sociolinguistics.

Mind the data gap(s): Investigating power in speech and language datasets

Current language technology is ubiquitous and directly influences individuals' lives worldwide. Given the recent trend in AI on training and constantly releasing new and powerful large language models (LLMs), there is a need to assess their biases and potential concrete consequences. While some studies have highlighted the shortcomings of these models, there is only little on the negative impact of LLMs on LGBTQIA+ individuals. In this paper, we investigated a state-of-the-art template-based approach for measuring the harmfulness of English LLMs sentence completion when the subjects belong to the LGBTQIA+ community. Our findings show that, on average, the most likely LLM-generated completion is an identity attack 13% of the time. Our results raise serious concerns about the applicability of these models in production environments.

Measuring Harmful Sentence Completion in Language Models for LGBTQIA+ Individuals

Deaf and hard of hearing individuals regularly rely on captioning while watching live TV. Live TV captioning is evaluated by regulatory agencies using various caption evaluation metrics. However, caption evaluation metrics are often not informed by preferences of DHH users or how meaningful the captions are. There is a need to construct caption evaluation metrics that take the relative importance of words in a transcript into account. We conducted correlation analysis between two types of word embeddings and human-annotated labeled word-importance scores in existing corpus. We found that normalized contextualized word embeddings generated using BERT correlated better with manually annotated importance scores than word2vec-based word embeddings. We make available a pairing of word embeddings and their human-annotated importance scores. We also provide proof-of-concept utility by training word importance models, achieving an F1-score of 0.57 in the 6-class word importance classification task.

Towards Automatic Curation of Antibiotic Resistance Genes via Statement Extraction from Scientific Papers: A Benchmark Dataset and Models

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Inter-annotator agreement is not the ceiling of machine learning performance: Evidence from a comprehensive set of simulations

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