Early cancer detection and treatment depend on the discovery of specific genes that cause cancer. The classification of genetic mutations was initially done manually. However, this process relies on pathologists and can be a time-consuming task. Therefore, to improve the precision of clinical interpretation, researchers have developed computational algorithms that leverage next-generation sequencing technologies for automated mutation analysis. This paper utilized four deep learning classification models with training collections of biomedical texts. These models comprise bidirectional encoder representations from transformers for Biomedical text mining (BioBERT), a specialized language model implemented for biological contexts. Impressive results in multiple tasks, including text classification, language inference, and question answering, can be obtained by simply adding an extra layer to the BioBERT model. Moreover, bidirectional encoder representations from transformers (BERT), long short-term memory (LSTM), and bidirectional LSTM (BiLSTM) have been leveraged to produce very good results in categorizing genetic mutations based on textual evidence. The dataset used in the work was created by Memorial Sloan Kettering Cancer Center (MSKCC), which contains several mutations. Furthermore, this dataset poses a major classification challenge in the Kaggle research prediction competitions. In carrying out the work, three challenges were identified: enormous text length, biased representation of the data, and repeated data instances. Based on the commonly used evaluation metrics, the experimental results show that the BioBERT model outperforms other models with an F1 score of 0.87 and 0.850 MCC, which can be considered as improved performance compared to similar results in the literature that have an F1 score of 0.70 achieved with the BERT model.

UNASSIGNED: Sentiment analysis has become a crucial area of research in natural language processing in recent years. The study aims to compare the performance of various sentiment analysis techniques, including lexicon-based, machine learning, Bi-LSTM, BERT, and GPT-3 approaches, using two commonly used datasets, IMDB reviews and Sentiment140. The objective is to identify the best-performing technique for an exemplar dataset, tweets associated with the WHO Framework Convention on Tobacco Control Ninth Conference of the Parties in 2021 (COP9).
UNASSIGNED: A two-stage evaluation was conducted. In the first stage, various techniques were compared on standard sentiment analysis datasets using standard evaluation metrics such as accuracy, F1-score, and precision. In the second stage, the best-performing techniques from the first stage were applied to partially annotated COP9 conference-related tweets.
UNASSIGNED: In the first stage, BERT achieved the highest F1-scores (0.9380 for IMDB and 0.8114 for Sentiment 140), followed by GPT-3 (0.9119 and 0.7913) and Bi-LSTM (0.8971 and 0.7778). In the second stage, GPT-3 performed the best for sentiment analysis on partially annotated COP9 conference-related tweets, with an F1-score of 0.8812.
UNASSIGNED: The study demonstrates the effectiveness of pre-trained models like BERT and GPT-3 for sentiment analysis tasks, outperforming traditional techniques on standard datasets. Moreover, the better performance of GPT-3 on the partially annotated COP9 tweets highlights its ability to generalize well to domain-specific data with limited annotations. This provides researchers and practitioners with a viable option of using pre-trained models for sentiment analysis in scenarios with limited or no annotated data across different domains.

BACKGROUND: In this paper, we present an automated method for article classification, leveraging the power of large language models (LLMs).
OBJECTIVE: The aim of this study is to evaluate the applicability of various LLMs based on textual content of scientific ophthalmology papers.
METHODS: We developed a model based on natural language processing techniques, including advanced LLMs, to process and analyze the textual content of scientific papers. Specifically, we used zero-shot learning LLMs and compared Bidirectional and Auto-Regressive Transformers (BART) and its variants with Bidirectional Encoder Representations from Transformers (BERT) and its variants, such as distilBERT, SciBERT, PubmedBERT, and BioBERT. To evaluate the LLMs, we compiled a data set (retinal diseases [RenD] ) of 1000 ocular disease-related articles, which were expertly annotated by a panel of 6 specialists into 19 distinct categories. In addition to the classification of articles, we also performed analysis on different classified groups to find the patterns and trends in the field.
RESULTS: The classification results demonstrate the effectiveness of LLMs in categorizing a large number of ophthalmology papers without human intervention. The model achieved a mean accuracy of 0.86 and a mean F1-score of 0.85 based on the RenD data set.
CONCLUSIONS: The proposed framework achieves notable improvements in both accuracy and efficiency. Its application in the domain of ophthalmology showcases its potential for knowledge organization and retrieval. We performed a trend analysis that enables researchers and clinicians to easily categorize and retrieve relevant papers, saving time and effort in literature review and information gathering as well as identification of emerging scientific trends within different disciplines. Moreover, the extendibility of the model to other scientific fields broadens its impact in facilitating research and trend analysis across diverse disciplines.

BACKGROUND: Research gaps refer to unanswered questions in the existing body of knowledge, either due to a lack of studies or inconclusive results. Research gaps are essential starting points and motivation in scientific research. Traditional methods for identifying research gaps, such as literature reviews and expert opinions, can be time consuming, labor intensive, and prone to bias. They may also fall short when dealing with rapidly evolving or time-sensitive subjects. Thus, innovative scalable approaches are needed to identify research gaps, systematically assess the literature, and prioritize areas for further study in the topic of interest.
OBJECTIVE: In this paper, we propose a machine learning-based approach for identifying research gaps through the analysis of scientific literature. We used the COVID-19 pandemic as a case study.
METHODS: We conducted an analysis to identify research gaps in COVID-19 literature using the COVID-19 Open Research (CORD-19) data set, which comprises 1,121,433 papers related to the COVID-19 pandemic. Our approach is based on the BERTopic topic modeling technique, which leverages transformers and class-based term frequency-inverse document frequency to create dense clusters allowing for easily interpretable topics. Our BERTopic-based approach involves 3 stages: embedding documents, clustering documents (dimension reduction and clustering), and representing topics (generating candidates and maximizing candidate relevance).
RESULTS: After applying the study selection criteria, we included 33,206 abstracts in the analysis of this study. The final list of research gaps identified 21 different areas, which were grouped into 6 principal topics. These topics were: \"virus of COVID-19,\" \"risk factors of COVID-19,\" \"prevention of COVID-19,\" \"treatment of COVID-19,\" \"health care delivery during COVID-19,\" \"and impact of COVID-19.\" The most prominent topic, observed in over half of the analyzed studies, was \"the impact of COVID-19.\"
CONCLUSIONS: The proposed machine learning-based approach has the potential to identify research gaps in scientific literature. This study is not intended to replace individual literature research within a selected topic. Instead, it can serve as a guide to formulate precise literature search queries in specific areas associated with research questions that previous publications have earmarked for future exploration. Future research should leverage an up-to-date list of studies that are retrieved from the most common databases in the target area. When feasible, full texts or, at minimum, discussion sections should be analyzed rather than limiting their analysis to abstracts. Furthermore, future studies could evaluate more efficient modeling algorithms, especially those combining topic modeling with statistical uncertainty quantification, such as conformal prediction.

Electronic health records (EHRs) in unstructured formats are valuable sources of information for research in both the clinical and biomedical domains. However, before such records can be used for research purposes, sensitive health information (SHI) must be removed in several cases to protect patient privacy. Rule-based and machine learning-based methods have been shown to be effective in deidentification. However, very few studies investigated the combination of transformer-based language models and rules.
The objective of this study is to develop a hybrid deidentification pipeline for Australian EHR text notes using rules and transformers. The study also aims to investigate the impact of pretrained word embedding and transformer-based language models.
In this study, we present a hybrid deidentification pipeline called OpenDeID, which is developed using an Australian multicenter EHR-based corpus called OpenDeID Corpus. The OpenDeID corpus consists of 2100 pathology reports with 38,414 SHI entities from 1833 patients. The OpenDeID pipeline incorporates a hybrid approach of associative rules, supervised deep learning, and pretrained language models.
The OpenDeID achieved a best F1-score of 0.9659 by fine-tuning the Discharge Summary BioBERT model and incorporating various preprocessing and postprocessing rules. The OpenDeID pipeline has been deployed at a large tertiary teaching hospital and has processed over 8000 unstructured EHR text notes in real time.
The OpenDeID pipeline is a hybrid deidentification pipeline to deidentify SHI entities in unstructured EHR text notes. The pipeline has been evaluated on a large multicenter corpus. External validation will be undertaken as part of our future work to evaluate the effectiveness of the OpenDeID pipeline.

The Transformer-based approaches to solving natural language processing (NLP) tasks such as BERT and GPT are gaining popularity due to their ability to achieve high performance. These approaches benefit from using enormous data sizes to create pre-trained models and the ability to understand the context of words in a sentence. Their use in the information retrieval domain is thought to increase effectiveness and efficiency. This paper demonstrates a BERT-based method (CASBERT) implementation to build a search tool over data annotated compositely using ontologies. The data was a collection of biosimulation models written using the CellML standard in the Physiome Model Repository (PMR). A biosimulation model structurally consists of basic entities of constants and variables that construct higher-level entities such as components, reactions, and the model. Finding these entities specific to their level is beneficial for various purposes regarding variable reuse, experiment setup, and model audit. Initially, we created embeddings representing compositely-annotated entities for constant and variable search (lowest level entity). Then, these low-level entity embeddings were vertically and efficiently combined to create higher-level entity embeddings to search components, models, images, and simulation setups. Our approach was general, so it can be used to create search tools with other data semantically annotated with ontologies - biosimulation models encoded in the SBML format, for example. Our tool is named Biosimulation Model Search Engine (BMSE).

Evidence-based medicine, the practice in which healthcare professionals refer to the best available evidence when making decisions, forms the foundation of modern healthcare. However, it relies on labour-intensive systematic reviews, where domain specialists must aggregate and extract information from thousands of publications, primarily of randomised controlled trial (RCT) results, into evidence tables. This paper investigates automating evidence table generation by decomposing the problem across two language processing tasks: named entity recognition, which identifies key entities within text, such as drug names, and relation extraction, which maps their relationships for separating them into ordered tuples. We focus on the automatic tabulation of sentences from published RCT abstracts that report the results of the study outcomes. Two deep neural net models were developed as part of a joint extraction pipeline, using the principles of transfer learning and transformer-based language representations. To train and test these models, a new gold-standard corpus was developed, comprising over 550 result sentences from six disease areas. This approach demonstrated significant advantages, with our system performing well across multiple natural language processing tasks and disease areas, as well as in generalising to disease domains unseen during training. Furthermore, we show these results were achievable through training our models on as few as 170 example sentences. The final system is a proof of concept that the generation of evidence tables can be semi-automated, representing a step towards fully automating systematic reviews.

BACKGROUND: The normalization of institution names is of great importance for literature retrieval, statistics of academic achievements, and evaluation of the competitiveness of research institutions. Differences in authors\' writing habits and spelling mistakes lead to various names of institutions, which affects the analysis of publication data. With the development of deep learning models and the increasing maturity of natural language processing methods, training a deep learning-based institution name normalization model can increase the accuracy of institution name normalization at the semantic level.
OBJECTIVE: This study aimed to train a deep learning-based model for institution name normalization based on the feature fusion of affiliation data from multisource literature, which would realize the normalization of institution name variants with the help of authority files and achieve a high specification accuracy after several rounds of training and optimization.
METHODS: In this study, an institution name normalization-oriented model was trained based on bidirectional encoder representations from transformers (BERT) and other deep learning models, including the institution classification model, institutional hierarchical relation extraction model, and institution matching and merging model. The model was then trained to automatically learn institutional features by pretraining and fine-tuning, and institution names were extracted from the affiliation data of 3 databases to complete the normalization process: Dimensions, Web of Science, and Scopus.
RESULTS: It was found that the trained model could achieve at least 3 functions. First, the model could identify the institution name that is consistent with the authority files and associate the name with the files through the unique institution ID. Second, it could identify the nonstandard institution name variants, such as singular forms, plural changes, and abbreviations, and update the authority files. Third, it could identify the unregistered institutions and add them to the authority files, so that when the institution appeared again, the model could identify and regard it as a registered institution. Moreover, the test results showed that the accuracy of the normalization model reached 93.79%, indicating the promising performance of the model for the normalization of institution names.
CONCLUSIONS: The deep learning-based institution name normalization model trained in this study exhibited high accuracy. Therefore, it could be widely applied in the evaluation of the competitiveness of research institutions, analysis of research fields of institutions, and construction of interinstitutional cooperation networks, among others, showing high application value.

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UNASSIGNED: In China, involution, which means pressure to out-compete other group members, has attracted public attention on Weibo. The new online connotation of involution empowered group cohesion among youth. Dissimilar to other crises, this crise also closely relates to group cohesion concept. However, few previous group cohesion-related studies focus on this critical concept. This study explains why and how youth created group cohesion online when facing involution. First, by examining the relationship between involution and group cohesion. Second, by examining whether youth are united in the online discussion of involution by investigating the generational gap. Following this, this study analyzes the different opinions to identify why this group cohesion occurs, how youth think about involution, and why they regard \"older adults\" as others. Lastly, this study analyzes how youth use hashtags to attract more youth to voice their opinions, consequently leading to greater group cohesion.
UNASSIGNED: By combining frontier computational methods with causation and axial coding, this study proposes a new way to in-depth analyze group cohesion on social media.
UNASSIGNED: The results indicate that involution triggers poor online group cohesion, and online involution-related hot issues trigger identity-based group cohesion. Additionally, youth are significantly more negative than older adults, and their expressions are full of identity-based construction. By stressing the social roots and blaming the \"other\" (older adult group), youth united together online. These findings indicated that a generation gap does indeed exist and that youth unite on social media by posting related hashtags via \"revealing social identity\" and \"positioning and becoming\" strategies.
UNASSIGNED: The findings stress that involution is related to poor group cohesion and that social media offers a new way to face the involution crisis. Youth will use hashtags to unite and blame imagined enemies, such as older adults and the upper class. These findings might assist in understanding interventions that lead to more group cohesion.