The process of matching patients with suitable clinical trials is essential for advancing medical research and providing optimal care. However, current approaches face challenges such as data standardization, ethical considerations, and a lack of interoperability between Electronic Health Records (EHRs) and clinical trial criteria. In this paper, we explore the potential of large language models (LLMs) to address these challenges by leveraging their advanced natural language generation capabilities to improve compatibility between EHRs and clinical trial descriptions. We propose an innovative privacy-aware data augmentation approach for LLM-based patient-trial matching (LLM-PTM), which balances the benefits of LLMs while ensuring the security and confidentiality of sensitive patient data. Our experiments demonstrate a 7.32% average improvement in performance using the proposed LLM-PTM method, and the generalizability to new data is improved by 12.12%. Additionally, we present case studies to further illustrate the effectiveness of our approach and provide a deeper understanding of its underlying principles.

Electronic health records (EHRs) store an extensive array of patient information, encompassing medical histories, diagnoses, treatments, and test outcomes. These records are crucial for enabling healthcare providers to make well-informed decisions regarding patient care. Summarizing clinical notes further assists healthcare professionals in pinpointing potential health risks and making better-informed decisions. This process contributes to reducing errors and enhancing patient outcomes by ensuring providers have access to the most pertinent and current patient data. Recent research has shown that incorporating prompts with large language models (LLMs) substantially boosts the efficacy of summarization tasks. However, we show that this approach also leads to increased output variance, resulting in notably divergent outputs even when prompts share similar meanings. To tackle this challenge, we introduce a model-agnostic Soft Prompt-Based Calibration (SPeC) pipeline that employs soft prompts to diminish variance while preserving the advantages of prompt-based summarization. Experimental findings on multiple clinical note tasks and LLMs indicate that our method not only bolsters performance but also effectively curbs variance for various LLMs, providing a more uniform and dependable solution for summarizing vital medical information.

The emergence of large language models (LLMs) has resulted in the production of LLM-generated texts that is highly sophisticated and almost indistinguishable from texts written by humans. However, this has also sparked concerns about the potential misuse of such texts, such as spreading misinformation and causing disruptions in the education system. Although many detection approaches have been proposed, a comprehensive understanding of the achievements and challenges is still lacking. This survey aims to provide an overview of existing LLM-generated text detection techniques and enhance the control and regulation of language generation models. Furthermore, we emphasize crucial considerations for future research, including the development of comprehensive evaluation metrics and the threat posed by open-source LLMs, to drive progress in the area of LLM-generated text detection.

Graph Neural Networks (GNNs) are gaining extensive attention for their application in graph data. However, the black-box nature of GNNs prevents users from understanding and trusting the models, thus hampering their applicability. Whereas explaining GNNs remains a challenge, most existing methods fall into approximation based and perturbation based approaches with suffer from faithfulness problems and unnatural artifacts, respectively. To tackle these problems, we propose DEGREE \degree to provide a faithful explanation for GNN predictions. By decomposing the information generation and aggregation mechanism of GNNs, DEGREE allows tracking the contributions of specific components of the input graph to the final prediction. Based on this, we further design a subgraph level interpretation algorithm to reveal complex interactions between graph nodes that are overlooked by previous methods. The efficiency of our algorithm can be further improved by utilizing GNN characteristics. Finally, we conduct quantitative and qualitative experiments on synthetic and real-world datasets to demonstrate the effectiveness of DEGREE on node classification and graph classification tasks.

This paper presents a comprehensive and practical guide for practitioners and end-users working with Large Language Models (LLMs) in their downstream natural language processing (NLP) tasks. We provide discussions and insights into the usage of LLMs from the perspectives of models, data, and downstream tasks. Firstly, we offer an introduction and brief summary of current GPT- and BERT-style LLMs. Then, we discuss the influence of pre-training data, training data, and test data. Most importantly, we provide a detailed discussion about the use and non-use cases of large language models for various natural language processing tasks, such as knowledge-intensive tasks, traditional natural language understanding tasks, natural language generation tasks, emergent abilities, and considerations for specific tasks.We present various use cases and non-use cases to illustrate the practical applications and limitations of LLMs in real-world scenarios. We also try to understand the importance of data and the specific challenges associated with each NLP task. Furthermore, we explore the impact of spurious biases on LLMs and delve into other essential considerations, such as efficiency, cost, and latency, to ensure a comprehensive understanding of deploying LLMs in practice. This comprehensive guide aims to provide researchers and practitioners with valuable insights and best practices for working with LLMs, thereby enabling the successful implementation of these models in a wide range of NLP tasks. A curated list of practical guide resources of LLMs, regularly updated, can be found at \url{https://github.com/Mooler0410/LLMsPracticalGuide}.

Detailed phenotype information is fundamental to accurate diagnosis and risk estimation of diseases. As a rich source of phenotype information, electronic health records (EHRs) promise to empower diagnostic variant interpretation. However, how to accurately and efficiently extract phenotypes from the heterogeneous EHR data remains a challenge. In this work, we present PheME, an Ensemble framework using Multi-modality data of structured EHRs and unstructured clinical notes for accurate Phenotype prediction. Firstly, we employ multiple deep neural networks to learn reliable representations from the sparse structured EHR data and redundant clinical notes. A multi-modal model then aligns multi-modal features onto the same latent space to predict phenotypes. Secondly, we leverage ensemble learning to combine outputs from single-modal models and multi-modal models to improve phenotype predictions. We choose seven diseases to evaluate the phenotyping performance of the proposed framework. Experimental results show that using multi-modal data significantly improves phenotype prediction in all diseases, the proposed ensemble learning framework can further boost the performance.

The huge supporting training data on the Internet has been a key factor in the success of deep learning models. However, this abundance of public-available data also raises concerns about the unauthorized exploitation of datasets for commercial purposes, which is forbidden by dataset licenses. In this paper, we propose a backdoor-based watermarking approach that serves as a general framework for safeguarding public-available data. By inserting a small number of watermarking samples into the dataset, our approach enables the learning model to implicitly learn a secret function set by defenders. This hidden function can then be used as a watermark to track down third-party models that use the dataset illegally. Unfortunately, existing backdoor insertion methods often entail adding arbitrary and mislabeled data to the training set, leading to a significant drop in performance and easy detection by anomaly detection algorithms. To overcome this challenge, we introduce a clean-label backdoor watermarking framework that uses imperceptible perturbations to replace mislabeled samples. As a result, the watermarking samples remain consistent with the original labels, making them difficult to detect. Our experiments on text, image, and audio datasets demonstrate that the proposed framework effectively safeguards datasets with minimal impact on original task performance. We also show that adding just 1% of watermarking samples can inject a traceable watermarking function and that our watermarking samples are stealthy and look benign upon visual inspection.

Recent advancements in large language models (LLMs) have led to the development of highly potent models like OpenAI's ChatGPT. These models have exhibited exceptional performance in a variety of tasks, such as question answering, essay composition, and code generation. However, their effectiveness in the healthcare sector remains uncertain. In this study, we seek to investigate the potential of ChatGPT to aid in clinical text mining by examining its ability to extract structured information from unstructured healthcare texts, with a focus on biological named entity recognition and relation extraction. However, our preliminary results indicate that employing ChatGPT directly for these tasks resulted in poor performance and raised privacy concerns associated with uploading patients' information to the ChatGPT API. To overcome these limitations, we propose a new training paradigm that involves generating a vast quantity of high-quality synthetic data with labels utilizing ChatGPT and fine-tuning a local model for the downstream task. Our method has resulted in significant improvements in the performance of downstream tasks, improving the F1-score from 23.37% to 63.99% for the named entity recognition task and from 75.86% to 83.59% for the relation extraction task. Furthermore, generating data using ChatGPT can significantly reduce the time and effort required for data collection and labeling, as well as mitigate data privacy concerns. In summary, the proposed framework presents a promising solution to enhance the applicability of LLM models to clinical text mining.

Liver transplant is an essential therapy performed for severe liver diseases. The fact of scarce liver resources makes the organ assigning crucial. Model for End-stage Liver Disease (MELD) score is a widely adopted criterion when making organ distribution decisions. However, it ignores post-transplant outcomes and organ/donor features. These limitations motivate the emergence of machine learning (ML) models. Unfortunately, ML models could be unfair and trigger bias against certain groups of people. To tackle this problem, this work proposes a fair machine learning framework targeting graft failure prediction in liver transplant. Specifically, knowledge distillation is employed to handle dense and sparse features by combining the advantages of tree models and neural networks. A two-step debiasing method is tailored for this framework to enhance fairness. Experiments are conducted to analyze unfairness issues in existing models and demonstrate the superiority of our method in both prediction and fairness performance.

Knowledge graph data are prevalent in real-world applications, and knowledge graph neural networks (KGNNs) are essential techniques for knowledge graph representation learning. Although KGNN effectively models the structural information from knowledge graphs, these frameworks amplify the underlying data bias that leads to discrimination towards certain groups or individuals in resulting applications. Additionally, as existing debiasing approaches mainly focus on the entity-wise bias, eliminating the multi-hop relational bias that pervasively exists in knowledge graphs remains an open question. However, it is very challenging to eliminate relational bias due to the sparsity of the paths that generate the bias and the non-linear proximity structure of knowledge graphs. To tackle the challenges, we propose Fair-KGNN, a KGNN framework that simultaneously alleviates multi-hop bias and preserves the proximity information of entity-to-relation in knowledge graphs. The proposed framework is generalizable to mitigate the relational bias for all types of KGNN. We develop two instances of Fair-KGNN incorporating with two state-of-the-art KGNN models, RGCN and CompGCN, to mitigate gender-occupation and nationality-salary bias. The experiments carried out on three benchmark knowledge graph datasets demonstrate that the Fair-KGNN can effectively mitigate unfair situations during representation learning while preserving the predictive performance of KGNN models.