OEMA: Ontology-Enhanced Multi-Agent Collaboration Framework for Zero-Shot Clinical Named Entity Recognition

Clinical named entity recognition (NER) is crucial for extracting information from electronic health records (EHRs), but supervised models like CRF and BioClinicalBERT require costly annotated data. While zero-shot NER with large language models (LLMs) reduces this dependency, it struggles with example selection granularity and integrating prompts with self-improvement. To address this, we propose OEMA, a zero-shot clinical NER framework using multi-agent collaboration. OEMA's three components are: a self-annotator generating examples, a discriminator filtering them via SNOMED CT, and a predictor using entity descriptions for accurate inference. On MTSamples and VAERS datasets, OEMA achieves state-of-the-art exact-match performance. Under related-match, it matches supervised BioClinicalBERT and surpasses CRF. OEMA addresses key zero-shot NER challenges through ontology-guided reasoning and multi-agent collaboration, achieving near-supervised performance and showing promise for clinical NLP applications.

TCM-FTP: Fine-Tuning Large Language Models for Herbal Prescription Prediction

Traditional Chinese medicine (TCM) relies on specific combinations of herbs in prescriptions to treat symptoms and signs, a practice that spans thousands of years. Predicting TCM prescriptions presents a fascinating technical challenge with practical implications. However, this task faces limitations due to the scarcity of high-quality clinical datasets and the intricate relationship between symptoms and herbs. To address these issues, we introduce DigestDS, a new dataset containing practical medical records from experienced experts in digestive system diseases. We also propose a method, TCM-FTP (TCM Fine-Tuning Pre-trained), to leverage pre-trained large language models (LLMs) through supervised fine-tuning on DigestDS. Additionally, we enhance computational efficiency using a low-rank adaptation technique. TCM-FTP also incorporates data augmentation by permuting herbs within prescriptions, capitalizing on their order-agnostic properties. Impressively, TCM-FTP achieves an F1-score of 0.8031, surpassing previous methods significantly. Furthermore, it demonstrates remarkable accuracy in dosage prediction, achieving a normalized mean square error of 0.0604. In contrast, LLMs without fine-tuning perform poorly. Although LLMs have shown capabilities on a wide range of tasks, this work illustrates the importance of fine-tuning for TCM prescription prediction, and we have proposed an effective way to do that.

A optimization framework for herbal prescription planning based on deep reinforcement learning

Treatment planning for chronic diseases is a critical task in medical artificial intelligence, particularly in traditional Chinese medicine (TCM). However, generating optimized sequential treatment strategies for patients with chronic diseases in different clinical encounters remains a challenging issue that requires further exploration. In this study, we proposed a TCM herbal prescription planning framework based on deep reinforcement learning for chronic disease treatment (PrescDRL). PrescDRL is a sequential herbal prescription optimization model that focuses on long-term effectiveness rather than achieving maximum reward at every step, thereby ensuring better patient outcomes. We constructed a high-quality benchmark dataset for sequential diagnosis and treatment of diabetes and evaluated PrescDRL against this benchmark. Our results showed that PrescDRL achieved a higher curative effect, with the single-step reward improving by 117% and 153% compared to doctors. Furthermore, PrescDRL outperformed the benchmark in prescription prediction, with precision improving by 40.5% and recall improving by 63%. Overall, our study demonstrates the potential of using artificial intelligence to improve clinical intelligent diagnosis and treatment in TCM.

Knowledge Graph Completion based on Tensor Decomposition for Disease Gene Prediction

Accurate identification of disease genes has consistently been one of the keys to decoding a disease's molecular mechanism. Most current approaches focus on constructing biological networks and utilizing machine learning, especially, deep learning to identify disease genes, but ignore the complex relations between entities in the biological knowledge graph. In this paper, we construct a biological knowledge graph centered on diseases and genes, and develop an end-to-end Knowledge graph completion model for Disease Gene Prediction using interactional tensor decomposition (called KDGene). KDGene introduces an interaction module between the embeddings of entities and relations to tensor decomposition, which can effectively enhance the information interaction in biological knowledge. Experimental results show that KDGene significantly outperforms state-of-the-art algorithms. Furthermore, the comprehensive biological analysis of the case of diabetes mellitus confirms KDGene's ability for identifying new and accurate candidate genes. This work proposes a scalable knowledge graph completion framework to identify disease candidate genes, from which the results are promising to provide valuable references for further wet experiments.

A Pre-training Framework for Knowledge Graph Completion

Knowledge graph completion (KGC) is one of the effective methods to identify new facts in knowledge graph. Except for a few methods based on graph network, most of KGC methods trend to be trained based on independent triples, while are difficult to take a full account of the information of global network connection contained in knowledge network. To address these issues, in this study, we propose a simple and effective Network-based Pre-training framework for knowledge graph completion (termed NetPeace), which takes into account the information of global network connection and local triple relationships in knowledge graph. Experiments show that in NetPeace framework, multiple KGC models yields consistent and significant improvements on benchmarks (e.g., 36.45% Hits@1 and 27.40% MRR improvements for TuckER on FB15k-237), especially dense knowledge graph. On the challenging low-resource task, NetPeace that benefits from the global features of KG achieves higher performance (104.03% MRR and 143.89% Hit@1 improvements at most) than original models.