In medical and social media domains, annotated corpora are often hard to distribute due to copyrights and privacy issues. To overcome this situation, we propose a new method to generate a surrogate corpus for a downstream task by using a text generation model. We chose a medical multi-label classification task, MedWeb, in which patient-generated short messages express multiple symptoms. We first fine-tuned text generation models with different prompting designs on the original corpus to obtain synthetic versions of that corpus. To assess the viability of the generated corpora for the downstream task, we compared the performance of multi-label classification models trained either on the original or the surrogate corpora. The results and the error analysis showed the difficulty of generating surrogate corpus in multi-label settings, suggesting text generation under complex conditions is not trivial. On the other hand, our experiment demonstrates that the generated corpus with a sentinel-based prompting is comparatively viable in a single-label (multiclass) classification setting.

Domain adaptation is crucial in the clinical domain since the performance of a model trained on one domain (source) degrades seriously when applied to another domain (target). However, conventional domain adaptation methods often cannot be applied due to data sharing restrictions on source data. Source-Free Domain Adaptation (SFDA) addresses this issue by only utilizing a source model and unlabeled target data to adapt to the target domain. In SFDA, self-training is the most widely applied method involving retraining models with target data using predictions from the source model as pseudo-labels. Nevertheless, this approach is prone to contain substantial numbers of errors in pseudo-labeling and might limit model performance in the target domain. In this paper, we propose a Source-Free Prototype-based Self-training (SFPS) aiming to improve the performance of self-training. SFPS generates prototypes without accessing source data and utilizes them for prototypical learning, namely prototype-based pseudo-labeling and contrastive learning. Also, we compare entropy-based, centroid-based, and class-weights-based prototype generation methods to identify the most effective formulation of the proposed method. Experimental results across various datasets demonstrate the effectiveness of the proposed method, consistently outperforming vanilla self-training. The comparison of various prototype-generation methods identifies the most reliable generation method that improves the source model persistently. Additionally, our analysis illustrates SFPS can successfully alleviate errors in pseudo-labeling.

User-generated data sources have gained significance in uncovering Adverse Drug Reactions (ADRs), with an increasing number of discussions occurring in the digital world. However, the existing clinical corpora predominantly revolve around scientific articles in English. This work presents a multilingual corpus of texts concerning ADRs gathered from diverse sources, including patient fora, social media, and clinical reports in German, French, and Japanese. Our corpus contains annotations covering 12 entity types, four attribute types, and 13 relation types. It contributes to the development of real-world multilingual language models for healthcare. We provide statistics to highlight certain challenges associated with the corpus and conduct preliminary experiments resulting in strong baselines for extracting entities and relations between these entities, both within and across languages.

Temporal relation annotation in the clinical domain is crucial yet challenging due to its workload and the medical expertise required. In this paper, we propose a novel annotation method that integrates event start-points ordering and question-answering (QA) as the annotation format. By focusing only on two points on a timeline, start-points ordering reduces ambiguity and simplifies the relation set to be considered during annotation. QA as annotation recasts temporal relation annotation into a reading comprehension task, allowing annotators to use natural language instead of the formalisms commonly adopted in temporal relation annotation. Based on our method, most of the relations in a document are inferable from a significantly smaller number of explicitly annotated relations, showing the efficiency of our proposed method. Using these inferred relations, we develop a temporal relation classification model that achieves a 0.72 F1 score. Also, by decomposing the annotation process into QA generation and QA validation, our method enables collaboration among medical experts and non-experts. We obtained high inter-annotator agreement (IAA) scores, which indicate the positive prospect of such collaboration in the annotation process. Our annotated corpus, annotation tool, and trained model are publicly available: https://github.com/seiji-shimizu/qa-start-ordering.

This paper provides an overview of Task 2 from the Social Media Mining for Health 2024 shared task (#SMM4H 2024), which focused on Named Entity Recognition (NER, Subtask 2a) and the joint task of NER and Relation Extraction (RE, Subtask 2b) for detecting adverse drug reactions (ADRs) in German, Japanese, and French texts written by patients. Participants were challenged with a few-shot learning scenario, necessitating models that can effectively generalize from limited annotated examples. Despite the diverse strategies employed by the participants, the overall performance across submissions from three teams highlighted significant challenges. The results underscored the complexity of extracting entities and relations in multi-lingual contexts, especially from the noisy and informal nature of user-generated content. Further research is required to develop robust systems capable of accurately identifying and associating ADR-related information in low-resource and multilingual settings.

For the past nine years, the Social Media Mining for Health Applications (#SMM4H) shared tasks have promoted community-driven development and evaluation of advanced natural language processing systems to detect, extract, and normalize health-related information in publicly available user-generated content. This year, #SMM4H included seven shared tasks in English, Japanese, German, French, and Spanish from Twitter, Reddit, and health forums. A total of 84 teams from 22 countries registered for #SMM4H, and 45 teams participated in at least one task. This represents a growth of 180% and 160% in registration and participation, respectively, compared to the last iteration. This paper provides an overview of the tasks and participating systems. The data sets remain available upon request, and new systems can be evaluated through the post-evaluation phase on CodaLab.

Entity Linking performance has a strong reliance on having a large quantity of high-quality annotated training data available. Yet, manual annotation of named entities, especially their boundaries, is ambiguous, error-prone, and raises many inconsistencies between annotators. While imprecise boundary annotation can degrade a model’s performance, there are applications where accurate extraction of entities’ surface form is not necessary. For those cases, a lenient annotation guideline could relieve the annotators’ workload and speed up the process. This paper presents a case study designed to verify the feasibility of such annotation process and evaluate the impact of boundary-relaxed annotation in an Entity Linking pipeline. We first generate a set of noisy versions of the widely used AIDA CoNLL-YAGO dataset by expanding the boundaries subsets of annotated entity mentions and then train three Entity Linking models on this data and evaluate the relative impact of imprecise annotation on entity recognition and disambiguation performances. We demonstrate that the magnitude of effects caused by noise in the Named Entity Recognition phase is dependent on both model complexity and noise ratio, while Entity Disambiguation components are susceptible to entity boundary imprecision due to strong vocabulary dependency.

We present a publicly available corpus with detailed annotations describing the core elements of clinical trials: Participants, Intervention, Control, and Outcomes. The corpus consists of 1011 abstracts of breast cancer randomized controlled trials extracted from the PubMed database. The corpus improves previous corpora by providing detailed annotations for outcomes to identify numeric texts that report the number of participants that experience specific outcomes. The corpus will be helpful for the development of systems for automatic extraction of data from randomized controlled trial literature to support evidence-based medicine. Additionally, we demonstrate the feasibility of the corpus by using two strong baselines for named entity recognition task. Most of the entities achieve F1 scores greater than 0.80 demonstrating the quality of the dataset.

In the field of Japanese medical information extraction, few analyzing tools are available and relation extraction is still an under-explored topic. In this paper, we first propose a novel relation annotation schema for investigating the medical and temporal relations between medical entities in Japanese medical reports. We experiment with the practical annotation scenarios by separately annotating two different types of reports. We design a pipeline system with three components for recognizing medical entities, classifying entity modalities, and extracting relations. The empirical results show accurate analyzing performance and suggest the satisfactory annotation quality, the superiority of the latest contextual embedding models. and the feasible annotation strategy for high-accuracy demand.

Disease name recognition and normalization is a fundamental process in biomedical text mining. Recently, neural joint learning of both tasks has been proposed to utilize the mutual benefits. While this approach achieves high performance, disease concepts that do not appear in the training dataset cannot be accurately predicted. This study introduces a novel end-to-end approach that combines span representations with dictionary-matching features to address this problem. Our model handles unseen concepts by referring to a dictionary while maintaining the performance of neural network-based models. Experiments using two major datasaets demonstrate that our model achieved competitive results with strong baselines, especially for unseen concepts during training.

This paper presents a prototype of a chat room that detects offensive expressions in a video live streaming chat in real time. Focusing on Twitch, one of the most popular live streaming platforms, we created a dataset for the task of detecting offensive expressions. We collected 2,000 chat posts across four popular game titles with genre diversity (e.g., competitive, violent, peaceful). To make use of the similarity in offensive expressions among different social media platforms, we adopted state-of-the-art models trained on offensive expressions from Twitter for our Twitch data (i.e., transfer learning). We investigated two similarity measurements to predict the transferability, textual similarity, and game-genre similarity. Our results show that the transfer of features from social media to live streaming is effective. However, the two measurements show less correlation in the transferability prediction.

Applying natural language processing (NLP) to medical and clinical texts can bring important social benefits by mining valuable information from unstructured text. A popular application for that purpose is named entity recognition (NER), but the annotation policies of existing clinical corpora have not been standardized across clinical texts of different types. This paper presents an annotation guideline aimed at covering medical documents of various types such as radiography interpretation reports and medical records. Furthermore, the annotation was designed to avoid burdensome requirements related to medical knowledge, thereby enabling corpus development without medical specialists. To achieve these design features, we specifically focus on critical lung diseases to stabilize linguistic patterns in corpora. After annotating around 1100 electronic medical records following the annotation scheme, we demonstrated its feasibility using an NER task. Results suggest that our guideline is applicable to large-scale clinical NLP projects.