Recognizing biomedical concepts in the text is vital for ontology refinement, knowledge graph construction, and concept relationship discovery. However, traditional concept recognition methods, relying on explicit mention identification, often fail to capture complex concepts not explicitly stated in the text. To overcome this limitation, we introduce MA-COIR, a framework that reformulates concept recognition as an indexing-recognition task. By assigning semantic search indexes (ssIDs) to concepts, MA-COIR resolves ambiguities in ontology entries and enhances recognition efficiency. Using a pretrained BART-based model fine-tuned on small datasets, our approach reduces computational requirements to facilitate adoption by domain experts. Furthermore, we incorporate large language model (LLM)-generated queries and synthetic data to improve recognition in low-resource settings. Experimental results on three scenarios (CDR, HPO, and HOIP) highlight the effectiveness of MA-COIR in recognizing both explicit and implicit concepts without the need for mention-level annotations during inference, advancing ontology-driven concept recognition in biomedical domain applications. Our code and constructed data are available at https://github.com/sl-633/macoir-master.

Automatic biomedical annotation is essential for advancing medical research, diagnosis, and treatment. However, it presents significant challenges, especially when entities are not explicitly mentioned in the text, leading to difficulties in extraction of relevant information. These challenges are intensified by unclear terminology, implicit background knowledge, and the lack of labeled training data. Annotating with a specific ontology adds another layer of complexity, as it requires aligning text with a predefined set of concepts and relationships. Manual annotation is time-consuming and expensive, highlighting the need for automated systems to handle large volumes of biomedical data efficiently. In this paper, we propose an entailment-based zero-shot text classification approach to annotate biomedical text passages using the Homeostasis Imbalance Process (HOIP) ontology. Our method reformulates the annotation task as a multi-class, multi-label classification problem and uses natural language inference to classify text into related HOIP processes. Experimental results show promising performance, especially when processes are not explicitly mentioned, highlighting the effectiveness of our approach for ontological annotation of biomedical literature.

With the emergence of new topics on social media as sources of rumor propagation, addressing the domain shift between the source and target domain and the target domain samples scarcity remains a crucial task in cross-domain rumor detection. Traditional deep learning-based methods and LLM-based methods are mostly focused on the in-domain condition, thus having poor performance in cross-domain setting. Existing domain adaptation rumor detection approaches ignore the data generalization differences and rely on a large amount of unlabeled target domain samples to achieve domain adaptation, resulting in less effective on emerging topic rumor detection. In this paper, we propose a Gradient Coherence guided Meta-Learning approach (GCML) for emerging topics rumor detection. Firstly, we calculate the task generalization score of each source task (sampled from source domain) from a gradient coherence perspective, and selectively learn more “generalizable” tasks that are more beneficial in adapting to the target domain. Secondly, we leverage meta-learning to alleviate the target domain samples scarcity, which utilizes task generalization scores to re-weight meta-test gradients and adaptively updates learning rate. Extensive experimental results on real-world datasets show that our method substantially outperforms SOTA baselines.

With the emergence of new topics on social media as sources of rumor dissemination, addressing the distribution shifts between source and target domains remains a crucial task in cross-domain rumor detection. Existing feature alignment methods, which aim to reduce the discrepancies between domains, are often susceptible to task interference during training. Additionally, data distribution alignment methods, which rely on existing data to synthesize new training samples, inherently introduce noise. To deal with these challenges, a new cross-domain rumor detection method, MONTROSE, is proposed. It combines LLM-driven Monte Carlo Tree Search (MCTS) data synthesis to generate high-quality synthetic data for the target domain and a domain-sharpness-aware (DSAM) self-refinement approach to train rumor detection models with these synthetic data effectively. Experiments demonstrate the superior performance of MONTROSE in cross-domain rumor detection.

Biomedical information extraction is crucial for advancing research, enhancing healthcare, and discovering treatments by efficiently analyzing extensive data. Given the extensive amount of biomedical data available, automated information extraction methods are necessary due to manual extraction’s labor-intensive, expertise-dependent, and costly nature. In this paper, we propose a novel two-stage system for information extraction where we annotate biomedical articles based on a specific ontology (HOIP). The major challenge is annotating relation between biomedical processes often not explicitly mentioned in text articles. Here, we first predict the candidate processes and then determine the relationships between these processes. The experimental results show promising outcomes in mention-agnostic process identification using Large Language Models (LLMs). In relation classification, BERT-based supervised models still outperform LLMs significantly. The end-to-end evaluation results suggest the difficulty of this task and room for improvement in both process identification and relation classification.