Ireland

Term clustering is important in biomedical knowledge graph construction.
Using similarities between terms embedding is helpful for term clustering.
State-of-the-art term embeddings leverage pretrained language models to encode terms, and use synonyms and relation knowledge from knowledge graphs to guide contrastive learning.
These embeddings provide close embeddings for terms belonging to the same concept.
However, from our probing experiments, these embeddings are not sensitive to minor textual differences which leads to failure for biomedical term clustering.
To alleviate this problem, we adjust the sampling strategy in pretraining term embeddings by providing dynamic hard positive and negative samples during contrastive learning to learn fine-grained representations which result in better biomedical term clustering.
We name our proposed method as CODER++, and it has been applied in clustering biomedical concepts in the newly released Biomedical Knowledge Graph named BIOS.

ACL 2022

Automatic Biomedical Term Clustering by Learning Fine-grained Term Representations

dynamic sampling

term clustering

contrastive learning

knowledge graph

## Welcome to NAACL 2022!
The Annual Meeting of the North American Chapter of the Association for Computational Linguistics (NAACL) is taking place July 10-15, 2022 as a hybrid event, in Seattle, WA and online. We are happy to welcome all of you to conference! 
 
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, keynote presentations, a plenary panel on the place of linguistics and symbolic structures in NLP, and an Industrial Track panel on Careers in NLP.
 
Posters (including Findings of NAACL 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 and will have an oral session and a poster session.
 
The program also features 6 Tutorials and 26 Workshops.
 
 We wish you a wonderful conference!
 
[The NAACL 2022 Organizing Committee](https://2022.naacl.org/committees/organization/)

NAACL 2022

2022 Annual Conference of the North American Chapter of the Association for Computational Linguistics

workshop paper

# 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) 
[**Mini Handbook**](https://drive.google.com/file/d/1qlBKl0wzmlVF1oCeMQl3BahLd9nLP5Ce/view?usp=sharing) 
[**Posters and Demo guides**](https://drive.google.com/file/d/1UucMAoCNncIOaH1rMMDa0owuG9qgvJTG/view?usp=sharing)

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). 

We study the zero-shot setting for the aspect-based scientific document summarization task. Summarizing scientific documents with respect to an aspect can remarkably improve document assistance systems and readers experience. However, existing large-scale datasets contain a limited variety of aspects, causing summarization models to over-fit to a small set of aspects and a specific domain. We establish baseline results in zero-shot performance (over unseen aspects and the presence of domain shift), paraphrasing, leave-one-out, and limited supervised samples experimental setups. We propose a self-supervised pre-training approach to enhance the zero-shot performance. We leverage the PubMed structured abstracts to create a biomedical aspect-based summarization dataset. Experimental results on the PubMed and FacetSum aspect-based datasets show promising performance when the model is pre-trained using unlabelled in-domain data.

Zero-Shot Aspect-Based Scientific Document Summarization using Self-Supervised Pre-training

We study the effect of seven data augmentation (DA) methods in factoid question answering, focusing on the biomedical domain, where obtaining training instances is particularly difficult. We experiment with data from the BIOASQ challenge, which we augment with training instances obtained from an artificial biomedical machine reading comprehension dataset, or via back-translation, information retrieval, word substitution based on WORD2VEC embeddings, or masked language modeling, question generation, or extending the given passage with additional context. We show that DA can lead to very significant performance gains, even when using large pre-trained Transformers, contributing to a broader discussion of if/when DA benefits large pre-trained models. One of the simplest DA methods, WORD2VEC-based word substitution, performed best and is recommended. We release our artificial training instances and code.

Data Augmentation for Biomedical Factoid Question Answering

We address a low-resource code-mixed (Spanish-Catalan) and domain-specific (Stroke) problem of clinical texts de-identification. We empirically find the strong presence of few-shot cross-lingual transfer in mBERT and apply it to our problem by annotating a few-shot training corpus and a development corpus. Our models achieved a 14%+ gain over zero-shot and have the potential for other low-resource applications.

Few-Shot Cross-lingual Transfer for Coarse-grained De-identification of Code-Mixed Clinical Texts

In-domain language model pretraining has been shown to benefit various domain-specific down-stream tasks. In the biomedical domain, natural language generation (NLG) tasks such as medical dialogue system are of critical importance, while understudied. We emphasize the lack of in-domain generative language model and the unsystematic generative downstream benchmarks. We introduce the generative language model BioBART that adapts BART to the biomedical domain and collate various biomedical language generation tasks for model evaluation.

BioBART: Pretraining and Evaluation of A Biomedical Generative Language Model

The introduction and experimental analysis of the proposed approach, Memory-aligned Knowledge Graph for Clinically Accurate RadiologyImage Report Generation.

Memory-aligned Knowledge Graph for Clinically Accurate Radiology Image Report Generation

Data augmentation is important in addressing data sparsity and low resources in NLP. Unlike data augmentation for other tasks such as sentence-level and sentence-pair ones, data augmentation for named entity recognition (NER) requires preserving the semantic of entities. To that end, in this paper we propose a simple semantic-based data augmentation method for biomedical NER. Our method leverages semantic information from pre-trained language models for both entity-level and sentence-level. Experimental results on two datasets: i2b2-2010 (English) and VietBioNER (Vietnamese) showed that the proposed method could improve NER performance.

Simple Semantic-based Data Augmentation for Named Entity Recognition in Biomedical Texts

Probing factual knowledge in Pre-trained Language Models (PLMs) using prompts has indirectly implied that language models (LMs) can be treated as knowledge bases. To this end, this phenomena has been effective, especially when these LMs are fine-tuned towards not just data, but also to the style or linguistic pattern of the prompts themselves. We observe that, satisfying a particular linguistic pattern in prompts is an unsustainable, time-consuming constraint in the probing task, especially because, they are often manually designed and the range of possible prompt template patterns can vary depending on the prompting task. To alleviate this constraint, we propose using a position-attention mechanism to capture positional information of each word in a prompt relative to the mask to be filled, hence avoiding the need to re-construct prompts when the prompts’ linguistic pattern changes. Using our approach, we demonstrate the ability of eliciting answers (in a case study on health outcome generation) to not only common prompt templates like Cloze and Prefix, but also rare ones too, such as Postfix and Mixed patterns whose masks are respectively at the start and in multiple random places of the prompt. More so, using various biomedical PLMs, our approach consistently outperforms a baseline in which the default PLMs representation is used to predict masked tokens.


Position-based Prompting for Health Outcome Generation

Text summarization (TS) is an important NLP task. Pre-trained Language Models (PLMs) have been used to improve the performance of TS. However, PLMs are limited by their need of labelled training data and by their attention mechanism, which often makes them unsuitable for use on long documents. To this end, we propose a hybrid, unsupervised, abstractive-extractive approach, in which we walk through a document, generating salient textual fragments representing its key points. We then select the most important sentences of the document by choosing the most similar sentences to the generated texts, calculated using BERTScore. We evaluate the efficacy of generating and using salient textual fragments to guide extractive summarization on documents from the biomedical and general scientific domains. We compare the performance between long and short documents using different generative text models, which are finetuned to generate relevant queries or document titles. We show that our hybrid approach out-performs existing unsupervised methods, as well as state-of-the-art supervised methods, despite not needing a vast amount of labelled training data.

GenCompareSum: a hybrid unsupervised summarization method using salience

Named entity recognition (NER) is one of the core technologies for knowledge acquisition from text and has been used for knowledge extraction of chemicals and medicine. 
As one of the NER improvement approaches, multitask learning that learns a model from multiple training data has been used. Among multitask learning, an auxiliary learning method, which uses training data of an auxiliary task for improving its target task, has shown higher NER performance than conventional multitask learning for improving all the tasks simultaneously. The conventional auxiliary learning method uses only one auxiliary training dataset. 
We propose Multiple Utilization of NER Corpora Helpful for Auxiliary BLESsing
(MUNCHABLES). MUNCHABLES utilizes multiple training datasets as auxiliary training data by the following methods : the first one is to fine-tune the NER model of the target task by sequentially performing auxiliary learning for each auxiliary training dataset, and the other is to use all training datasets in one auxiliary learning. We evaluate MUNCHABLES on eight chemical/biomedical/scientific domain NER tasks, where seven training datasets are used as auxiliary training data. The experiment results show that our proposed methods achieve higher NER performance than conventional multi-task learning methods on average and that NER performance can be improved by using multiple auxiliary training data. Furthermore, the proposed models outperform stateof-the-art models on the datasets

Auxiliary Learning for Named Entity Recognition with Multiple Auxiliary Biomedical Training Data

Self-supervised pre-training methods have brought remarkable breakthroughs in the understanding of text, image, and speech. Recent developments in genomics has also adopted these pre-training methods for genome understanding. However, they focus only on understanding haploid sequences, which hinders their applicability towards understanding genetic variations, also known as single nucleotide polymorphisms (SNPs), which is crucial for genome-wide association study. In this paper, we introduce SNP2Vec, a scalable self-supervised pre-training approach for understanding SNP. We apply SNP2Vec to perform long-sequence genomics modeling, and we evaluate the effectiveness of our approach on predicting Alzheimer's disease risk in a Chinese cohort. Our approach significantly outperforms existing polygenic risk score methods and all other baselines, including the model that is trained entirely with haploid sequences. We release our code and dataset on https://github.com/HLTCHKUST/snp2vec.

Automatic Biomedical Term Clustering by Learning Fine-grained Term Representations

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