Understanding the genetic basis of disease is a fundamental aspect of medical research, as genes are the classic units of heredity and play a crucial role in biological function. Identifying associations between genes and diseases is critical for diagnosis, prevention, prognosis, and drug development. Genes that encode proteins with similar sequences are often implicated in related diseases, as proteins causing identical or similar diseases tend to show limited variation in their sequences. Predicting gene-disease association (GDA) requires time-consuming and expensive experiments on a large number of potential candidate genes. Although methods have been proposed to predict associations between genes and diseases using traditional machine learning algorithms and graph neural networks, these approaches struggle to capture the deep semantic information within the genes and diseases and are dependent on training data. To alleviate this issue, we propose a novel GDA prediction model named FusionGDA, which utilizes a pre-training phase with a fusion module to enrich the gene and disease semantic representations encoded by pre-trained language models. Multi-modal representations are generated by the fusion module, which includes rich semantic information about two heterogeneous biomedical entities: protein sequences and disease descriptions. Subsequently, the pooling aggregation strategy is adopted to compress the dimensions of the multi-modal representation. In addition, FusionGDA employs a pre-training phase leveraging a contrastive learning loss to extract potential gene and disease features by training on a large public GDA dataset. To rigorously evaluate the effectiveness of the FusionGDA model, we conduct comprehensive experiments on five datasets and compare our proposed model with five competitive baseline models on the DisGeNet-Eval dataset. Notably, our case study further demonstrates the ability of FusionGDA to discover hidden associations effectively. The complete code and datasets of our experiments are available at https://github.com/ZhaohanM/FusionGDA.

BACKGROUND: The urgency and complexity of emergency room (ER) settings require precise and swift decision-making processes for patient care. Ensuring the timely execution of critical examinations and interventions is vital for reducing diagnostic errors, but the literature highlights a need for innovative approaches to optimize diagnostic accuracy and patient outcomes. In response, our study endeavors to create predictive models for timely examinations and interventions by leveraging the patient\'s symptoms and vital signs recorded during triage, and in so doing, augment traditional diagnostic methodologies.
METHODS: Focusing on four key areas-medication dispensing, vital interventions, laboratory testing, and emergency radiology exams, the study employed Natural Language Processing (NLP) and seven advanced machine learning techniques. The research was centered around the innovative use of BioClinicalBERT, a state-of-the-art NLP framework.
RESULTS: BioClinicalBERT emerged as the superior model, outperforming others in predictive accuracy. The integration of physiological data with patient narrative symptoms demonstrated greater effectiveness compared to models based solely on textual data. The robustness of our approach was confirmed by an Area Under the Receiver Operating Characteristic curve (AUROC) score of 0.9.
CONCLUSIONS: The findings of our study underscore the feasibility of establishing a decision support system for emergency patients, targeting timely interventions and examinations based on a nuanced analysis of symptoms. By using an advanced natural language processing technique, our approach shows promise for enhancing diagnostic accuracy. However, the current model is not yet fully mature for direct implementation into daily clinical practice. Recognizing the imperative nature of precision in the ER environment, future research endeavors must focus on refining and expanding predictive models to include detailed timely examinations and interventions. Although the progress achieved in this study represents an encouraging step towards a more innovative and technology-driven paradigm in emergency care, full clinical integration warrants further exploration and validation.

OBJECTIVE: Active learning (AL) has rarely integrated diversity-based and uncertainty-based strategies into a dynamic sampling framework for clinical named entity recognition (NER). Machine-assisted annotation is becoming popular for creating gold-standard labels. This study investigated the effectiveness of dynamic AL strategies under simulated machine-assisted annotation scenarios for clinical NER.
METHODS: We proposed 3 new AL strategies: a diversity-based strategy (CLUSTER) based on Sentence-BERT and 2 dynamic strategies (CLC and CNBSE) capable of switching from diversity-based to uncertainty-based strategies. Using BioClinicalBERT as the foundational NER model, we conducted simulation experiments on 3 medication-related clinical NER datasets independently: i2b2 2009, n2c2 2018 (Track 2), and MADE 1.0. We compared the proposed strategies with uncertainty-based (LC and NBSE) and passive-learning (RANDOM) strategies. Performance was primarily measured by the number of edits made by the annotators to achieve a desired target effectiveness evaluated on independent test sets.
RESULTS: When aiming for 98% overall target effectiveness, on average, CLUSTER required the fewest edits. When aiming for 99% overall target effectiveness, CNBSE required 20.4% fewer edits than NBSE did. CLUSTER and RANDOM could not achieve such a high target under the pool-based simulation experiment. For high-difficulty entities, CNBSE required 22.5% fewer edits than NBSE to achieve 99% target effectiveness, whereas neither CLUSTER nor RANDOM achieved 93% target effectiveness.
CONCLUSIONS: When the target effectiveness was set high, the proposed dynamic strategy CNBSE exhibited both strong learning capabilities and low annotation costs in machine-assisted annotation. CLUSTER required the fewest edits when the target effectiveness was set low.

In the development of the Power Industry Internet of Things, the security of data interaction has always been an important challenge. In the power-based blockchain Industrial Internet of Things, node data interaction involves a large amount of sensitive data. In the current anti-leakage strategy for power business data interaction, regular expressions are used to identify sensitive data for matching. This approach is only suitable for simple structured data. For the processing of unstructured data, there is a lack of practical matching strategies. Therefore, this paper proposes a deep learning-based anti-leakage method for power business data interaction, aiming to ensure the security of power business data interaction between the State Grid business platform and third-party platforms. This method combines named entity recognition technologies and comprehensively uses regular expressions and the DeBERTa (Decoding-enhanced BERT with disentangled attention)-BiLSTM (Bidirectional Long Short-Term Memory)-CRF (Conditional Random Field) model. This method is based on the DeBERTa (Decoding-enhanced BERT with disentangled attention) model for pre-training feature extraction. It extracts sequence context semantic features through the BiLSTM, and finally obtains the global optimal through the CRF layer tag sequence. Sensitive data matching is performed on interactive structured and unstructured data to identify privacy-sensitive information in the power business. The experimental results show that the F1 score of the proposed method in this paper for identifying sensitive data entities using the CLUENER 2020 dataset reaches 81.26%, which can effectively prevent the risk of power business data leakage and provide innovative solutions for the power industry to ensure data security.

With the rapid progress in Natural Language Processing (NLP), Pre-trained Language Models (PLM) such as BERT, BioBERT, and ChatGPT have shown great potential in various medical NLP tasks. This paper surveys the cutting-edge achievements in applying PLMs to various medical NLP tasks. Specifically, we first brief PLMS and outline the research of PLMs in medicine. Next, we categorise and discuss the types of tasks in medical NLP, covering text summarisation, question-answering, machine translation, sentiment analysis, named entity recognition, information extraction, medical education, relation extraction, and text mining. For each type of task, we first provide an overview of the basic concepts, the main methodologies, the advantages of applying PLMs, the basic steps of applying PLMs application, the datasets for training and testing, and the metrics for task evaluation. Subsequently, a summary of recent important research findings is presented, analysing their motivations, strengths vs weaknesses, similarities vs differences, and discussing potential limitations. Also, we assess the quality and influence of the research reviewed in this paper by comparing the citation count of the papers reviewed and the reputation and impact of the conferences and journals where they are published. Through these indicators, we further identify the most concerned research topics currently. Finally, we look forward to future research directions, including enhancing models\' reliability, explainability, and fairness, to promote the application of PLMs in clinical practice. In addition, this survey also collect some download links of some model codes and the relevant datasets, which are valuable references for researchers applying NLP techniques in medicine and medical professionals seeking to enhance their expertise and healthcare service through AI technology.

The increasing prevalence of overcrowding in Emergency Departments (EDs) threatens the effective delivery of urgent healthcare. Mitigation strategies include the deployment of monitoring systems capable of tracking and managing patient disposition to facilitate appropriate and timely care, which subsequently reduces patient revisits, optimizes resource allocation, and enhances patient outcomes. This study used ∼ 250,000 emergency department visit records from Taipei Medical University-Shuang Ho Hospital to develop a natural language processing model using BlueBERT, a biomedical domain-specific pre-trained language model, to predict patient disposition status and unplanned readmissions. Data preprocessing and the integration of both structured and unstructured data were central to our approach. Compared to other models, BlueBERT outperformed due to its pre-training on a diverse range of medical literature, enabling it to better comprehend the specialized terminology, relationships, and context present in ED data. We found that translating Chinese-English clinical narratives into English and textualizing numerical data into categorical representations significantly improved the prediction of patient disposition (AUROC = 0.9014) and 72-hour unscheduled return visits (AUROC = 0.6475). The study concludes that the BlueBERT-based model demonstrated superior prediction capabilities, surpassing the performance of prior patient disposition predictive models, thus offering promising applications in the realm of ED clinical practice.

Pre-trained Language Model (PLM) is nowadays the mainstay of Unsupervised Sentence Representation Learning (USRL). However, PLMs are sensitive to the frequency information of words from their pre-training corpora, resulting in anisotropic embedding space, where the embeddings of high-frequency words are clustered but those of low-frequency words disperse sparsely. This anisotropic phenomenon results in two problems of similarity bias and information bias, lowering the quality of sentence embeddings. To solve the problems, we fine-tune PLMs by leveraging the frequency information of words and propose a novel USRL framework, namely Sentence Representation Learning with Frequency-induced Adversarial tuning and Incomplete sentence filtering (Slt-fai). We calculate the word frequencies over the pre-training corpora of PLMs and assign words thresholding frequency labels. With them, (1) we incorporate a similarity discriminator used to distinguish the embeddings of high-frequency and low-frequency words, and adversarially tune the PLM with it, enabling to achieve uniformly frequency-invariant embedding space; and (2) we propose a novel incomplete sentence detection task, where we incorporate an information discriminator to distinguish the embeddings of original sentences and incomplete sentences by randomly masking several low-frequency words, enabling to emphasize the more informative low-frequency words. Our Slt-fai is a flexible and plug-and-play framework, and it can be integrated with existing USRL techniques. We evaluate Slt-fai with various backbones on benchmark datasets. Empirical results indicate that Slt-fai can be superior to the existing USRL baselines.

Accurate classification of membrane proteins like ion channels and transporters is critical for elucidating cellular processes and drug development. We present DeepPLM_mCNN, a novel framework combining Pretrained Language Models (PLMs) and multi-window convolutional neural networks (mCNNs) for effective classification of membrane proteins into ion channels and ion transporters. Our approach extracts informative features from protein sequences by utilizing various PLMs, including TAPE, ProtT5_XL_U50, ESM-1b, ESM-2_480, and ESM-2_1280. These PLM-derived features are then input into a mCNN architecture to learn conserved motifs important for classification. When evaluated on ion transporters, our best performing model utilizing ProtT5 achieved 90% sensitivity, 95.8% specificity, and 95.4% overall accuracy. For ion channels, we obtained 88.3% sensitivity, 95.7% specificity, and 95.2% overall accuracy using ESM-1b features. Our proposed DeepPLM_mCNN framework demonstrates significant improvements over previous methods on unseen test data. This study illustrates the potential of combining PLMs and deep learning for accurate computational identification of membrane proteins from sequence data alone. Our findings have important implications for membrane protein research and drug development targeting ion channels and transporters. The data and source codes in this study are publicly available at the following link: https://github.com/s1129108/DeepPLM_mCNN.

BACKGROUND: Cell-type annotation of single-cell RNA-sequencing (scRNA-seq) data is a hallmark of biomedical research and clinical application. Current annotation tools usually assume the simultaneous acquisition of well-annotated data, but without the ability to expand knowledge from new data. Yet, such tools are inconsistent with the continuous emergence of scRNA-seq data, calling for a continuous cell-type annotation model. In addition, by their powerful ability of information integration and model interpretability, transformer-based pre-trained language models have led to breakthroughs in single-cell biology research. Therefore, the systematic combining of continual learning and pre-trained language models for cell-type annotation tasks is inevitable.
RESULTS: We herein propose a universal cell-type annotation tool, called CANAL, that continuously fine-tunes a pre-trained language model trained on a large amount of unlabeled scRNA-seq data, as new well-labeled data emerges. CANAL essentially alleviates the dilemma of catastrophic forgetting, both in terms of model inputs and outputs. For model inputs, we introduce an experience replay schema that repeatedly reviews previous vital examples in current training stages. This is achieved through a dynamic example bank with a fixed buffer size. The example bank is class-balanced and proficient in retaining cell-type-specific information, particularly facilitating the consolidation of patterns associated with rare cell types. For model outputs, we utilize representation knowledge distillation to regularize the divergence between previous and current models, resulting in the preservation of knowledge learned from past training stages. Moreover, our universal annotation framework considers the inclusion of new cell types throughout the fine-tuning and testing stages. We can continuously expand the cell-type annotation library by absorbing new cell types from newly arrived, well-annotated training datasets, as well as automatically identify novel cells in unlabeled datasets. Comprehensive experiments with data streams under various biological scenarios demonstrate the versatility and high model interpretability of CANAL.
BACKGROUND: An implementation of CANAL is available from https://github.com/aster-ww/CANAL-torch.
BACKGROUND: dengmh@pku.edu.cn.
BACKGROUND: Supplementary data are available at Journal Name online.

The drug discovery process is demanding and time-consuming, and machine learning-based research is increasingly proposed to enhance efficiency. A significant challenge in this field is predicting whether a drug molecule\'s structure will interact with a target protein. A recent study attempted to address this challenge by utilizing an encoder that leverages prior knowledge of molecular and protein structures, resulting in notable improvements in the prediction performance of the drug-target interactions task. Nonetheless, the target encoders employed in previous studies exhibit computational complexity that increases quadratically with the input length, thereby limiting their practical utility. To overcome this challenge, we adopt a hint-based learning strategy to develop a compact and efficient target encoder. With the adaptation parameter, our model can blend general knowledge and target-oriented knowledge to build features of the protein sequences. This approach yielded considerable performance enhancements and improved learning efficiency on three benchmark datasets: BIOSNAP, DAVIS, and Binding DB. Furthermore, our methodology boasts the merit of necessitating only a minimal Video RAM (VRAM) allocation, specifically 7.7GB, during the training phase (16.24% of the previous state-of-the-art model). This ensures the feasibility of training and inference even with constrained computational resources.