United States

In this work, we employ a transformer-based Seq2Seq model for generat-
ing the conclusion section of German radiology reports. The model is initialized with the pretrained parameters of a German BERT model and fine-tuned in our downstream task on our domain data. We proposed two strategies to improve the factual correctness of the model. In the first method, next to the abstractive learning
objective, we introduce an extraction learning objective to train the decoder in the model to both generate one summary sequence and extract the key findings from the source input. The second approach is to integrate the pointer mechanism into the transformer-based Seq2Seq model. The pointer network helps the Seq2Seq model to choose between generating tokens from the vocabulary or copying parts from the source input during generation. The results of the automatic and human evaluations show that the enhanced Seq2Seq model is capable of generating human-like radiology conclusions and that the improved models effectively reduce the factual errors in the generations despite the small amount of training data.

NAACL 2022

Fine-tuning BERT models for summarizing German radiology findings

clinical nlp in german

radiology findings summarization

abstractive summarization

# 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)

ACL 2022

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

## 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/)

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

In this work, cross-linguistic span prediction based on contextualized word embedding models is used together with neural machine translation (NMT) to transfer and apply the state-of-the-art models in natural language processing (NLP) to a low-resource language clinical corpus. Two directions are evaluated: (a) English models can be applied to translated texts to subsequently transfer the predicted annotations to the source language and (b) existing high-quality annotations can be transferred beyond translation and then used to train NLP models in the target language. Effectiveness and loss of transmission is evaluated using the German Berlin-Tübingen-Oncology Corpus (BRONCO) dataset with transferred external data from NCBI disease, SemEval-2013 drug-drug interaction (DDI) and i2b2/VA 2010 data. The use of English models for translated clinical texts has always involved attempts to take full advantage of the benefits associated with them (large pre-trained biomedical word embeddings). To improve advances in this area, we provide a general-purpose pipeline to transfer any annotated BRAT or CoNLL format to various target languages. For the entity class medication, good results were obtained with 0.806 F1-score after re-alignment. Limited success occurred in the diagnosis and treatment class with results just below 0.5 F1-score due to differences in annotation guidelines.

Cross-Language Transfer of High-Quality Annotations: Combining Neural Machine Translation with Cross-Linguistic Span Alignment to Apply NER to Clinical Texts in a Low-Resource Language

Decision support systems based on clinical notes have the potential to improve patient care by pointing doctors towards overseen risks. Predicting a patient's outcome is an essential part of such systems, for which the use of deep neural networks has shown promising results. However, the patterns learned by these networks are mostly opaque and previous work revealed both reproduction of systemic biases and unexpected behavior for out-of-distribution patients. For application in clinical practice it is crucial to be aware of such behavior. We thus introduce a testing framework that evaluates clinical models regarding certain changes in the input. The framework helps to understand learned patterns and their influence on model decisions. In this work, we apply it to analyse the change in behavior with regard to the patient characteristics gender, age and ethnicity. Our evaluation of three current clinical NLP models demonstrates the concrete effects of these characteristics on the models' decisions. They show that model behavior varies drastically even when fine-tuned on the same data with similar AUROC score. These results exemplify the need for a broader communication of model behavior in the clinical domain.

What Do You See in this Patient? Behavioral Testing of Clinical NLP Models

Existing question answering (QA) datasets derived from electronic health records (EHR) are artificially generated and consequently fail to capture realistic physician information needs. We present Discharge Summary Clinical Questions (DiSCQ), a newly curated question dataset composed of 2,000+ questions paired with the snippets of text (triggers) that prompted each question. The questions are generated by medical experts from 100+ MIMIC-III discharge summaries. We analyze this dataset to characterize the types of information sought by medical experts. We also train baseline models for trigger detection and question generation (QG), paired with unsupervised answer retrieval over EHRs. Our baseline model is able to generate high quality questions in over 62% of cases when prompted with human selected triggers. We release this dataset (and all code to reproduce baseline model results) to facilitate further research into realistic clinical QA and QG.

Learning to Ask Like a Physician

Although there are many clinical and biomedical language models for the English language, there is still a significant lack of models for Spanish. In this presentation, we introduce Clinical Flair, the first Spanish language model trained on real diagnoses from the Chilean public healthcare system. Taking the Named Entity Recognition task as a case study, we show that contextualized embeddings retrieved from our domain-specific language model outperform the results of the general domain model by a wide margin. In addition, we show that training a language model on real diagnoses may be more beneficial than training on electronic health records.

Clinical Flair: A Pre-Trained Language Model for Spanish Clinical Natural Language Processing

Recent studies show that neural natural processing models for medical code prediction suffer from a label imbalance issue. This study aims to investigate further imbalance in a medical code prediction dataset in terms of demographic variables and analyse performance differences in demographic groups. We use sample-based metrics to correctly evaluate the performance in terms of the data subject. Also, a simple label distance metric is proposed to quantify the difference in the label distribution between a group and the entire data. Our analysis results reveal that the model performs differently towards different demographic groups: significant differences between age groups and between insurance types are observed. Interestingly, we found a weak positive correlation between the number of training data of the group and the performance of the group. However, a strong negative correlation between the label distance of the group and the performance of the group is observed. This result suggests that the model tends to perform poorly in the group whose label distribution is different from the global label distribution of the training data set. Further analysis of the model performance is required to identify the cause of these differences and to improve the model building.

An exploratory data analysis: the performance differences of a medical code prediction system on different demographic groups

Sequence-to-sequence models are appealing because they allow both encoder and decoder to be shared across many tasks by formulating those tasks as text-to-text problems. Despite recently reported successes of such models, we find that engineering input/output representations for such text-to-text models is challenging. On the Clinical TempEval 2016 relation extraction task, the most natural choice of output representations, where relations are spelled out in simple predicate logic statements, did not lead to good performance. We explore a variety of input/output representations, with the most successful prompting one event at a time, and achieving results competitive with standard pairwise temporal relation extraction systems.

Exploring Text Representations for Generative Temporal Relation Extraction

The lack of resources for languages in the Americas has proven to be a problem for the creation of digital systems such as machine translation, search engines, chat bots, and more. The scarceness of digital resources for a language causes a higher impact on populations where the language is spoken by millions of people. We introduce the first official large combined corpus for deep learning of an indigenous South American low-resource language spoken by millions called Quechua. Specifi-
cally, our curated corpus is created from text gathered from the southern region of Peru where a dialect of Quechua is spoken that has not traditionally been used for digital systems as a target dialect in the past. In order to make our work repeatable by others, we also offer a public, pre-trained, BERT model called QuBERT which is the largest linguistic model ever trained for any Quechua type, not just the south-
ern region dialect. We furthermore test our corpus and its corresponding BERT model on two major tasks: (1) named-entity recognition (NER) and (2) part-of-speech (POS) tagging by using state-of-the-art techniques where we achieve results comparable to other work on higher-resource languages. In this article, we
describe the methodology, challenges, and results from the creation of QuBERT which is on on par with other state-of-the-art multilingual models for natural language processing achieving between 71 and 74% F1 score on NER and
84–87% on POS tasks.

Introducing QuBERT: A Large Monolingual Corpus and BERT Model for Southern Quechua

The distant supervision (DS) paradigm has been widely used for relation extraction (RE) to alleviate the need for expensive annotations. However, it suffers from noisy labels, which leads to worse performance than models trained on human-annotated data, even when trained using hundreds of times more data. We present a systematic study on the use of natural lan- guage inference (NLI) to improve distantly su- pervised document-level RE. We apply NLI in three scenarios: (i) as a filter for denoising DS labels, (ii) as a filter for model prediction, and (iii) as a standalone RE model. Our re- sults show that NLI filtering consistently im- proves performance, reducing the performance gap with a model trained on human-annotated data by 2.3 F1.

Improving Distantly Supervised Document-Level Relation Extraction Through Natural Language Inference

Training a tagger for Named Entity Recognition (NER) requires a substantial amount of labeled data in the task domain.
Manual labeling is a tedious and complicated task.
Semi-supervised learning methods can reduce the quantity of labeled data necessary to train a model.
However, these methods require large quantities of unlabeled data, which remains an issue in many cases.


We address this problem by generating unlabeled data.
Large language models have proven to be powerful tools for text generation.
We use their generative capacity to produce new sentences and variations of the sentences of our available data.
This generation method, combined with a semi-supervised method, is evaluated on CoNLL and I2B2.
We prepare both of these corpora to simulate a low resource setting.
We obtain significant improvements for semi-supervised learning with synthetic data against supervised learning on natural data.


Generating unlabelled data for a tri-training approach in a low resourced NER task

Text segmentation and extraction from unstructured documents can provide business researchers with a wealth of new information on firms and their behaviors. However, the most valuable text is often difficult to extract consistently due to substantial variations in how content can appear from document to document. Thus, the most successful way to extract this content has been through costly crowdsourcing and training of manual workers. We propose the Assisted Neural Text Segmentation (ANTS) framework to identify pertinent text in unstructured documents from a small set of labeled examples. ANTS leverages deep learning and transfer learning architectures to empower researchers to identify relevant text with minimal manual coding. Using a real world sample of accounting documents, we identify targeted sections 96% of the time using only 5 training examples.

Fine-tuning BERT models for summarizing German radiology findings

Downloads

Next from NAACL 2022

Cross-Language Transfer of High-Quality Annotations: Combining Neural Machine Translation with Cross-Linguistic Span Alignment to Apply NER to Clinical Texts in a Low-Resource Language

Similar lecture

Should We Trust This Summary? Bayesian Abstractive Summarization to The Rescue

Stay up to date with the latest Underline news!

PRESENTATIONS

CONFERENCES

COMPANY

RESOURCES

Fine-tuning BERT models for summarizing German radiology findings

.css-70qvj9{display:-webkit-box;display:-webkit-flex;display:-ms-flexbox;display:flex;-webkit-align-items:center;-webkit-box-align:center;-ms-flex-align:center;align-items:center;}Downloads

Next from NAACL 2022

Cross-Language Transfer of High-Quality Annotations: Combining Neural Machine Translation with Cross-Linguistic Span Alignment to Apply NER to Clinical Texts in a Low-Resource Language

Similar lecture

Should We Trust This Summary? Bayesian Abstractive Summarization to The Rescue

Stay up to date with the latest Underline news!

PRESENTATIONS

CONFERENCES

COMPANY

RESOURCES

Downloads