A Question Answering Based Pipeline for Comprehensive Chinese EHR Information Extraction

Electronic health records (EHRs) hold significant value for research and applications. As a new way of information extraction, question answering (QA) can extract more flexible information than conventional methods and is more accessible to clinical researchers, but its progress is impeded by the scarcity of annotated data. In this paper, we propose a novel approach that automatically generates training data for transfer learning of QA models. Our pipeline incorporates a preprocessing module to handle challenges posed by extraction types that are not readily compatible with extractive QA frameworks, including cases with discontinuous answers and many-to-one relationships. The obtained QA model exhibits excellent performance on subtasks of information extraction in EHRs, and it can effectively handle few-shot or zero-shot settings involving yes-no questions. Case studies and ablation studies demonstrate the necessity of each component in our design, and the resulting model is deemed suitable for practical use.

CAREForMe: Contextual Multi-Armed Bandit Recommendation Framework for Mental Health

The COVID-19 pandemic has intensified the urgency for effective and accessible mental health interventions in people's daily lives. Mobile Health (mHealth) solutions, such as AI Chatbots and Mindfulness Apps, have gained traction as they expand beyond traditional clinical settings to support daily life. However, the effectiveness of current mHealth solutions is impeded by the lack of context-awareness, personalization, and modularity to foster their reusability. This paper introduces CAREForMe, a contextual multi-armed bandit (CMAB) recommendation framework for mental health. Designed with context-awareness, personalization, and modularity at its core, CAREForMe harnesses mobile sensing and integrates online learning algorithms with user clustering capability to deliver timely, personalized recommendations. With its modular design, CAREForMe serves as both a customizable recommendation framework to guide future research, and a collaborative platform to facilitate interdisciplinary contributions in mHealth research. We showcase CAREForMe's versatility through its implementation across various platforms (e.g., Discord, Telegram) and its customization to diverse recommendation features.

High-throughput Biomedical Relation Extraction for Semi-Structured Web Articles Empowered by Large Language Models

Objective: To develop a high-throughput biomedical relation extraction system that takes advantage of the large language models' (LLMs) reading comprehension ability and biomedical world knowledge in a scalable and evidential manner. Methods: We formulate the relation extraction task as a simple binary classification problem for large language models such as ChatGPT. Specifically, LLMs make the decision based on the external corpus and its world knowledge, giving the reason for the judgment to factual verification. This method is tailored for semi-structured web articles, wherein we designate the main title as the tail entity and explicitly incorporate it into the context, and the potential head entities are matched based on a biomedical thesaurus. Moreover, lengthy contents are sliced into text chunks, embedded, and retrieved with additional embedding models, ensuring compatibility with the context window size constraints of available open-source LLMs. Results: Using an open-source LLM, we extracted 304315 relation triplets of three distinct relation types from four reputable biomedical websites. To assess the efficacy of the basic pipeline employed for biomedical relation extraction, we curated a benchmark dataset annotated by a medical expert. Evaluation results indicate that the pipeline exhibits performance comparable to that of GPT-4. Case studies further illuminate challenges faced by contemporary LLMs in the context of biomedical relation extraction for semi-structured web articles. Conclusion: The proposed method has demonstrated its effectiveness in leveraging the strengths of LLMs for high-throughput biomedical relation extraction. Its adaptability is evident, as it can be seamlessly extended to diverse semi-structured biomedical websites, facilitating the extraction of various types of biomedical relations with ease.

CoRTEx: Contrastive Learning for Representing Terms via Explanations with Applications on Constructing Biomedical Knowledge Graphs

Objective: Biomedical Knowledge Graphs play a pivotal role in various biomedical research domains. Concurrently, term clustering emerges as a crucial step in constructing these knowledge graphs, aiming to identify synonymous terms. Due to a lack of knowledge, previous contrastive learning models trained with Unified Medical Language System (UMLS) synonyms struggle at clustering difficult terms and do not generalize well beyond UMLS terms. In this work, we leverage the world knowledge from Large Language Models (LLMs) and propose Contrastive Learning for Representing Terms via Explanations (CoRTEx) to enhance term representation and significantly improves term clustering. Materials and Methods: The model training involves generating explanations for a cleaned subset of UMLS terms using ChatGPT. We employ contrastive learning, considering term and explanation embeddings simultaneously, and progressively introduce hard negative samples. Additionally, a ChatGPT-assisted BIRCH algorithm is designed for efficient clustering of a new ontology. Results: We established a clustering test set and a hard negative test set, where our model consistently achieves the highest F1 score. With CoRTEx embeddings and the modified BIRCH algorithm, we grouped 35,580,932 terms from the Biomedical Informatics Ontology System (BIOS) into 22,104,559 clusters with O(N) queries to ChatGPT. Case studies highlight the model's efficacy in handling challenging samples, aided by information from explanations. Conclusion: By aligning terms to their explanations, CoRTEx demonstrates superior accuracy over benchmark models and robustness beyond its training set, and it is suitable for clustering terms for large-scale biomedical ontologies.

The Internet of Responsibilities-Connecting Human Responsibilities using Big Data and Blockchain

Accountability in the workplace is critically important and remains a challenging problem, especially with respect to workplace safety management. In this paper, we introduce a novel notion, the Internet of Responsibilities, for accountability management. Our method sorts through the list of responsibilities with respect to hazardous positions. The positions are interconnected using directed acyclic graphs (DAGs) indicating the hierarchy of responsibilities in the organization. In addition, the system detects and collects responsibilities, and represents risk areas in terms of the positions of the responsibility nodes. Finally, an automatic reminder and assignment system is used to enforce a strict responsibility control without human intervention. Using blockchain technology, we further extend our system with the capability to store, recover and encrypt responsibility data. We show that through the application of the Internet of Responsibility network model driven by Big Data, enterprise and government agencies can attain a highly secured and safe workplace. Therefore, our model offers a combination of interconnected responsibilities, accountability, monitoring, and safety which is crucial for the protection of employees and the success of organizations.

EHRDiff: Exploring Realistic EHR Synthesis with Diffusion Models

Electronic health records (EHR) contain vast biomedical knowledge and are rich resources for developing precise medicine systems. However, due to privacy concerns, there are limited high-quality EHR data accessible to researchers hence hindering the advancement of methodologies. Recent research has explored using generative modelling methods to synthesize realistic EHR data, and most proposed methods are based on the generative adversarial network (GAN) and its variants for EHR synthesis. Although GAN-style methods achieved state-of-the-art performance in generating high-quality EHR data, such methods are hard to train and prone to mode collapse. Diffusion models are recently proposed generative modelling methods and set cutting-edge performance in image generation. The performance of diffusion models in realistic EHR synthesis is rarely explored. In this work, we explore whether the superior performance of diffusion models can translate to the domain of EHR synthesis and propose a novel EHR synthesis method named EHRDiff. Through comprehensive experiments, EHRDiff achieves new state-of-the-art performance for the quality of synthetic EHR data and can better protect private information in real training EHRs in the meanwhile.

Generative Biomedical Entity Linking via Knowledge Base-Guided Pre-training and Synonyms-Aware Fine-tuning

Entities lie in the heart of biomedical natural language understanding, and the biomedical entity linking (EL) task remains challenging due to the fine-grained and diversiform concept names. Generative methods achieve remarkable performances in general domain EL with less memory usage while requiring expensive pre-training. Previous biomedical EL methods leverage synonyms from knowledge bases (KB) which is not trivial to inject into a generative method. In this work, we use a generative approach to model biomedical EL and propose to inject synonyms knowledge in it. We propose KB-guided pre-training by constructing synthetic samples with synonyms and definitions from KB and require the model to recover concept names. We also propose synonyms-aware fine-tuning to select concept names for training, and propose decoder prompt and multi-synonyms constrained prefix tree for inference. Our method achieves state-of-the-art results on several biomedical EL tasks without candidate selection which displays the effectiveness of proposed pre-training and fine-tuning strategies.

BioBART: Pretraining and Evaluation of A Biomedical Generative Language Model

Pretrained language models have served as important backbones for natural language processing. Recently, in-domain pretraining has been shown to benefit various domain-specific downstream tasks. In the biomedical domain, natural language generation (NLG) tasks are of critical importance, while understudied. Approaching natural language understanding (NLU) tasks as NLG achieves satisfying performance in the general domain through constrained language generation or language prompting. We emphasize the lack of in-domain generative language models and the unsystematic generative downstream benchmarks in the biomedical domain, hindering the development of the research community. In this work, we introduce the generative language model BioBART that adapts BART to the biomedical domain. We collate various biomedical language generation tasks including dialogue, summarization, entity linking, and named entity recognition. BioBART pretrained on PubMed abstracts has enhanced performance compared to BART and set strong baselines on several tasks. Furthermore, we conduct ablation studies on the pretraining tasks for BioBART and find that sentence permutation has negative effects on downstream tasks.

Automatic Biomedical Term Clustering by Learning Fine-grained Term Representations

Term clustering is important in biomedical knowledge graph construction. Using similarities between terms embedding is helpful for term clustering. State-of-the-art term embeddings leverage pretrained language models to encode terms, and use synonyms and relation knowledge from knowledge graphs to guide contrastive learning. These embeddings provide close embeddings for terms belonging to the same concept. However, from our probing experiments, these embeddings are not sensitive to minor textual differences which leads to failure for biomedical term clustering. To alleviate this problem, we adjust the sampling strategy in pretraining term embeddings by providing dynamic hard positive and negative samples during contrastive learning to learn fine-grained representations which result in better biomedical term clustering. We name our proposed method as CODER++, and it has been applied in clustering biomedical concepts in the newly released Biomedical Knowledge Graph named BIOS.