Ireland

Biomedical Named Entity Recognition (BM-NER) is one of the most important tasks in the field of biomedical text mining. Most work so far on this task has not focused on identification of discontinuous and overlapping entities, even though they are present in significant fractions in real-life biomedical datasets.

In this paper, we introduce a novel annotation schema to capture complex entities, and explore the effects of distant supervision on our deep-learning sequence labelling model. For BMNER task, our annotation schema outperforms other BIO-based annotation schemes on the same model. We also achieve higher F1-scores than state-of-the-art models on multiple corpora without fine-tuning embeddings, highlighting the efficacy of neural feature extraction using our model.

ACL 2022

Biomedical NER using Novel Schema and Distant Supervision

discontitnuous entities

biomedical named entities

distant supervision

# 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). 

workshop paper

Research papers reflect scientific advances. Citations are widely used in research publications to support the new findings and show their benefits, while also regulating the information flow to make the contents clearer for the audience. A citation in a research article refers to the information's source, but not the specific text span from that source article. In biomedical research articles, this task is challenging as the same chemical or biological component can be represented in multiple ways in different papers from various domains. This paper suggests a mechanism for linking citing sentences in a publication with cited sentences in referenced sources. The framework presented here pairs the citing sentence with all of the sentences in the reference text, and then tries to retrieve the semantically equivalent pairs. These semantically related sentences from the reference paper are chosen as the cited statements. This effort involves designing a citation linkage framework utilizing sequential and tree-structured siamese deep learning models. This paper also provides a method to create an automatically generated corpus for such a task.

BioCite: A Deep Learning-based Citation Linkage Framework for Biomedical Research Articles

Generating a summary from findings has been recently explored (Zhang et al., 2018, 2020) in note types such as radiology reports that typically have short length. In this work, we focus on echocardiogram notes that are longer and more complex compared to previous note types. We formally define the task of echocardiography conclusion generation (EchoGen) as generating a conclusion given the findings section, with emphasis on key cardiac findings. To promote the development of EchoGen methods, we present a new benchmark, which consists of two datasets collected from two hospitals. We further compare both standard and state-of-the-art methods on this new benchmark, with an emphasis on factual consistency. To accomplish this, we develop a tool to automatically extract concept-attribute tuples from the text. We then propose an evaluation metric, FactComp, to compare concept-attribute tuples between the human reference and generated conclusions. Both automatic and human evaluations show that there is still a significant gap between human-written and machine-generated conclusions on echo reports in terms of factuality and overall quality.

EchoGen: Generating Conclusions from Echocardiogram Notes

A wealth of important clinical information lies untouched in the Electronic Health Record, often in the form of unstructured textual documents. For patients with Epilepsy, such information includes outcome measures like Seizure Frequency and Dates of Last Seizure, key parameters that guide all therapy for these patients. Transformer models have been able to extract such outcome measures from unstructured clinical note text as sentences with human-like accuracy; however, these sentences are not yet usable in a quantitative analysis for large-scale studies. In this study, we developed a pipeline to quantify these outcome measures. We used text summarization models to convert unstructured sentences into specific formats, and then employed rules-based quantifiers to calculate seizure frequencies and dates of last seizure. We demonstrated that our pipeline of models does not excessively propagate errors and we analyzed its mistakes. We anticipate that our methods can be generalized outside of epilepsy to other disorders to drive large-scale clinical research.

Quantifying Clinical Outcome Measures in Patients with Epilepsy Using the Electronic Health Record

Biomedical relation extraction, aiming to automatically discover high-quality and semantic relations between the entities from free text, is becoming a vital step for automated knowledge discovery. Pretrained language models have achieved impressive performance on various natural language processing tasks, including relation extraction. In this paper, we perform extensive empirical comparisons of encoder-only transformers with the encoder-decoder transformer, specifically T5, on ten public biomedical relation extraction datasets. We study the relation extraction task from four major biomedical tasks, namely chemical-protein relation extraction, disease-protein relation extraction, drug-drug interaction, and protein-protein interaction. We also explore the use of multi-task fine-tuning to investigate the correlation among major biomedical relation extraction tasks. We
report performance (micro F-score) using T5, BioBERT and PubMedBERT, demonstrating that T5 and multi-task learning can improve the performance of the biomedical relation extraction task.

Comparing Encoder-Only and Encoder-Decoder Transformers for Relation Extraction from Biomedical Texts: An Empirical Study on Ten Benchmark Datasets

Electronic health records contain valuable information about symptoms, diagnosis, treatment and outcomes of the treatments of individual patients. However, the records may also contain information that can reveal the identity of the patients. Removing these identifiers - the Protected Health Information (PHI) - can protect the identity of the patient. Automatic de-identification is a process which employs machine learning techniques to detect and remove PHI. However, automatic techniques are imperfect in their precision and introduce noise into the data. This study examines the impact of this noise on the utility of Swedish de-identified clinical data by using human evaluators and by training and testing BERT models. Our results indicate that de-identification does not harm the utility for clinical NLP and that human evaluators are less sensitive to noise from de-identification than expected.

Utility Preservation of Clinical Text After De-Identification

Medical document coding is the process of assigning labels from a structured label space (ontology – e.g., ICD-9) to medical documents. This process is laborious, costly, and error-prone. In recent years, efforts have been made to automate this process with neural models. The label spaces are large (in the order of thousands of labels) and follow a big-head long-tail label distribution, giving rise to few-shot and zero-shot scenarios. Previous efforts tried to address these scenarios within the model, leading to improvements on rare labels, but worse results on frequent ones. We propose data augmentation and synthesis techniques in order to address these scenarios. We further introduce an analysis technique for this setting inspired by confusion matrices. This analysis technique points to the positive impact of data augmentation and synthesis, but also highlights more general issues of confusion within families of codes, and underprediction.

Horses to Zebras: Ontology-Guided Data Augmentation and Synthesis for ICD-9 Coding

Conversational bots have become nontraditional methods for therapy among
individuals suffering from psychological illnesses. Leveraging deep neural generative
language models, we propose a deep trainable neural conversational model for therapyoriented response generation. We leverage transfer learning methods during training on therapy and counseling based data from Reddit and AlexanderStreet. This was done to adapt existing generative models – GPT2 and DIALOGPT – to the task of automated dialog generation. Through quantitative evaluation of the linguistic quality, we observe that the dialog generation model - DIALOGPT (345M) with transfer learning on video data attains scores similar to a human response baseline. However, human evaluation of responses by conversational bots show mostly signs of generic advice or information sharing instead of therapeutic interaction.

Conversational Bots for Psychotherapy: A Study of Generative Transformer Models Using Domain-specific Dialogues

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

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

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.

Biomedical NER using Novel Schema and Distant Supervision

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