Large Language Models Evaluation for PubMed Extractive Summarisation

Biomedical text summarization is a critical task for comprehension of an ever-growing amount of biomedical literature. Pre-trained language models (PLMs) with transformer-based architectures have been shown to greatly improve performance in biomedical text mining tasks. However, existing methods for text summarization generally fine-tune PLMs on the target corpora directly and do not consider how fine-grained domain knowledge, such as PICO elements used in evidence-based medicine, can help to identify the context needed for generating coherent summaries. To fill the gap, we propose KeBioSum, a novel knowledge infusion training framework, and experiment using a number of PLMs as bases, for the task of extractive summarization on biomedical literature. We investigate generative and discriminative training techniques to fuse domain knowledge (i.e., PICO elements) into knowledge adapters and apply adapter fusion to efficiently inject the knowledge adapters into the basic PLMs for fine-tuning the extractive summarization task. Experimental results from the extractive summarization task on three biomedical literature datasets show that existing PLMs (BERT, RoBERTa, BioBERT, and PubMedBERT) are improved by incorporating the KeBioSum knowledge adapters, and our model outperforms the strong baselines.

In this investigation, we propose a solution for the author’s gender identification task called AGI-P. This task has several real-world applications across different fields, such as marketing and advertising, forensic linguistics, sociology, recommendation systems, language processing, historical analysis, education, and language learning. We created a new dataset to evaluate our proposed method. The dataset is balanced in terms of gender using a random sampling method and consists of 1944 samples in total. We use accuracy as an evaluation measure and compare the performance of the proposed solution (AGI-P) against state-of-the-art machine learning classifiers and fine-tuned pre-trained multilingual language models such as DistilBERT, mBERT, XLM-RoBERTa, and Multilingual DEBERTa. In this regard, we also propose a customized fine-tuning strategy that improves the accuracy of the pre-trained language models for the author gender identification task. Our extensive experimental studies reveal that our solution (AGI-P) outperforms the well-known machine learning classifiers and fine-tuned pre-trained multilingual language models with an accuracy level of 92.03%. Moreover, the pre-trained multilingual language models, fine-tuned with the proposed customized strategy, outperform the fine-tuned pre-trained language models using an out-of-the-box fine-tuning strategy. The codebase and the corpus will be publicly available for scholars in this area upon publication.

Korean is the native and official language spoken by Chinese-Korean people, and Weibo is a social media software with a huge number of users in China. Currently, there is few studies related to sentiment analysis of Korean-language Weibo texts posted by Chinese-Korean users. In this paper, we propose a sentiment classification method for Chinese-Korean Weibo based on pre-trained language model and transfer learning. Firstly, we crawled the Chinese-Korean Weibo data from Sina Weibo and label them with sentiment to get the Chinese-Korean Weibo sentiment analysis (CKWSA) dataset. Secondly, to solve the problem of few training samples of the Chinese-Korean Weibo sentiment analysis dataset, we fine-tune the classifier based on the pre-trained Korean language model on the Korean Twitter sentiment analysis dataset to obtain the Korean Twitter sentiment classification model; and further fine-tune the model on CKWSA dataset to get Chinese-Korean Weibo sentiment classification model. The experiments show that the proposed classification method based on pre-trained language model and transfer learning has great performance, and there is an improvement compared other baselines on the Chinese-Korean Weibo sentiment analysis dataset.

Continuous professional development of science teachers is closely related to their ability to reflect on their science lessons. For teachers to effectively reflect on their lesson, they need opportunities to make meaningful teaching-related experiences and receive guiding feedback for their reflections during initial teacher education. A sensible means to provide reflection opportunities for teachers is through written reflection assignments. However, assessing written reflections is conceptually challenging and resource-intensive. Recent developments suggest that artificial intelligence (AI) might provide novel opportunities for science teacher education and assessing written reflections. Consequently, we investigate ways in which AI in the form of a large language model can be utilized in a specific science teacher training program. The potential of AI for the use in higher education have been highlighted in recent years. However, it is noted that large language models oftentimes are too generic to be useful in specific science teacher education contexts. To address this issue, we used a pre-trained large language model and fine-tuned it to provide individualized feedback for pre-service physics teachers’ written reflection and investigated to which degree contextual factors impact the classification accuracy. Our results show that the pre-trained language model allowed a sufficient classification and that the classification accuracy can be improved by context specification. Our study highlights opportunities and challenges when utilizing AI, in particular large language models, for reflective writing analytics in science education.

Transfer learning with large pretrained transformer-based language models like BERT has become a dominating approach for most NLP tasks. Simply fine-tuning those large language models on downstream tasks or combining it with task-specific pretraining is often not robust. In particular, the performance considerably varies as the random seed changes or the number of pretraining and/or fine-tuning iterations varies, and the fine-tuned model is vulnerable to adversarial attack. We propose a simple yet effective adapter-based approach to mitigate these issues. Specifically, we insert small bottleneck layers (i.e., adapter) within each layer of a pretrained model, then fix the pretrained layers and train the adapter layers on the downstream task data, with (1) task-specific unsupervised pretraining and then (2) task-specific supervised training (e.g., classification, sequence labeling). Our experiments demonstrate that such a training scheme leads to improved stability and adversarial robustness in transfer learning to various downstream tasks.

This paper describes the models designated for the MEDIQA 2019 shared tasks by the team PANLP. We take advantages of the recent advances in pre-trained bidirectional transformer language models such as BERT (Devlin et al., 2018) and MT-DNN (Liu et al., 2019b). We find that pre-trained language models can significantly outperform traditional deep learning models. Transfer learning from the NLI task to the RQE task is also experimented, which proves to be useful in improving the results of fine-tuning MT-DNN large. A knowledge distillation process is implemented, to distill the knowledge contained in a set of models and transfer it into an single model, whose performance turns out to be comparable with that obtained by the ensemble of that set of models. Finally, for test submissions, model ensemble and a re-ranking process are implemented to boost the performances. Our models participated in all three tasks and ranked the 1st place for the RQE task, and the 2nd place for the NLI task, and also the 2nd place for the QA task.

Antimicrobial peptides (AMPs) are vital components of innate immunotherapy. Existing approaches mainly rely on either deep learning for the automatic extraction of sequence features or traditional manual amino acid features combined with machine learning. The peptide sequence contains symmetrical sequence motifs or repetitive amino acid patterns, which may be related to the function and structure of the peptide. Recently, the advent of large language models has significantly boosted the representational power of sequence pattern features. In light of this, we present a novel AMP predictor called UniproLcad, which integrates three prominent protein language models—ESM-2, ProtBert, and UniRep—to obtain a more comprehensive representation of protein features. UniproLcad utilizes deep learning networks, encompassing the bidirectional long and short memory network (Bi-LSTM) and one-dimensional convolutional neural networks (1D-CNN), while also integrating an attention mechanism to enhance its capabilities. These deep learning frameworks, coupled with pre-trained language models, efficiently extract multi-view features from antimicrobial peptide sequences and assign attention weights to them. Through ten-fold cross-validation and independent testing, UniproLcad demonstrates competitive performance in the field of antimicrobial peptide identification. This integration of diverse language models and deep learning architectures enhances the accuracy and reliability of predicting antimicrobial peptides, contributing to the advancement of computational methods in this field.

With the success of down streaming task using English pre-trained language model, the pre-trained Chinese language model is also necessary to get better performance of Chinese NLP tasks. Unlike the English language, Chinese has its special characters such as glyph information. So in this article, we propose the Chinese pre-trained language model named StyleBERT which incorporate the following embedding information to enhance the savvy of language model, such as word, pinyin, five stroke and chaizi. The experiments show that the model achieves well performances on a wide range of Chinese NLP tasks.

Homonymy can easily raise lexical ambiguity due to the misunderstanding of its multiple senses.Correct recognition of homonym sense greatly relies on its surrounding context.This ambiguous nature makes homonyms an appropriate testbed for examining the contextualization capability of pre-trained (PLM) and large language models (LLMs).Considering the impact of part of speech (POS) on homonym disambiguation and the prevalence of English-focused studies in word embedding research, this study extends to Chinese and provides a comprehensive layer-wise analysis of homonym representations in both languages, spanning same and different POS categories, across four families of PLMs/LLMs (BERT, GPT-2, Llama 3, Qwen 2.5).Through the creation of a synthetic dataset and computation of disambiguation score (D-Score), we found that: (1) no universal layer depth excels in differentiating homonym representations; (2) bidirectional models produce better contextualized homonym representations compared to much larger autoregressive models; (3) most importantly, POS affects homonym representations in models in ways that differ from human research findings.The individual differences between LLMs uncovered in our study challenge the simplistic understanding of their inner workings.This reveals a compelling research frontier: conducting controlled experiments with purposefully manipulated inputs to enhance the interpretability of LLMs.We have made our dataset and codes available publicly at https://github.com/neurothew/ exploring-homonym-rep-in-llm.

Pre-trained language models have brought significant improvements in performance in a variety of natural language processing tasks. Most existing models performing state-of-the-art results have shown their approaches in the separate perspectives of data processing, pre-training tasks, neural network modeling, or fine-tuning. In this paper, we demonstrate how the approaches affect performance individually, and that the language model performs the best results on a specific question answering task when those approaches are jointly considered in pre-training models. In particular, we propose an extended pre-training task, and a new neighbor-aware mechanism that attends neighboring tokens more to capture the richness of context for pre-training language modeling. Our best model achieves new state-of-the-art results of 95.7% F1 and 90.6% EM on SQuAD 1.1 and also outperforms existing pre-trained language models such as RoBERTa, ALBERT, ELECTRA, and XLNet on the SQuAD 2.0 benchmark.

Since the development and wide use of pretrained language models (PLMs), several approaches have been applied to boost their performance on downstream tasks in specific domains, such as biomedical or scientific domains. Additional pre-training with in-domain texts is the most common approach for providing domain-specific knowledge to PLMs. However, these pre-training methods require considerable in-domain data and training resources and a longer training time. Moreover, the training must be re-performed whenever a new PLM emerges. In this study, we propose a domain knowledge transferring (DoKTra) framework for PLMs without additional in-domain pretraining. Specifically, we extract the domain knowledge from an existing in-domain pretrained language model and transfer it to other PLMs by applying knowledge distillation. In particular, we employ activation boundary distillation, which focuses on the activation of hidden neurons. We also apply an entropy regularization term in both teacher training and distillation to encourage the model to generate reliable output probabilities, and thus aid the distillation. By applying the proposed DoKTra framework to downstream tasks in the biomedical, clinical, and financial domains, our student models can retain a high percentage of teacher performance and even outperform the teachers in certain tasks. Our code is available at https://github.com/DMCB-GIST/DoKTra.

Advances in machine learning have made it possible to perform various text and speech processing tasks, such as automatic speech recognition (ASR), in an end-to-end (E2E) manner.E2E approaches utilizing pre-trained models are gaining attention for conserving training data and resources.However, most of their applications in ASR involve only one of either a pre-trained speech or a language model.This paper proposes integrating a pre-trained speech representation model and a large language model (LLM) for E2E ASR.The proposed model enables the optimization of the entire ASR process, including acoustic feature extraction and acoustic and language modeling, by combining pre-trained models with a bridge network and also enables the application of remarkable developments in LLM utilization, such as parameter-efficient domain adaptation and inference optimization.Experimental results demonstrate that the proposed model achieves a performance comparable to that of modern E2E ASR models by utilizing powerful pre-training models with the proposed integrated approach.

JointMatcher: Numerically-aware entity matching using pre-trained language models with attention concentration

Depression is a serious mental health disorder that poses a major public health concern in Thailand and have a profound impact on individuals' physical and mental health. In addition, the lack of number to mental health services and limited number of psychiatrists in Thailand make depression particularly challenging to diagnose and treat, leaving many individuals with the condition untreated. Recent studies have explored the use of natural language processing to enable access to the classification of depression, particularly with a trend toward transfer learning from pre-trained language model. In this study, we attempted to evaluate the effectiveness of using XLM-RoBERTa, a pre-trained multi-lingual language model supporting the Thai language, for the classification of depression from a limited set of text transcripts from speech responses. Twelve Thai depression assessment questions were developed to collect text transcripts of speech responses to be used with XLM-RoBERTa in transfer learning. The results of transfer learning with text transcription from speech responses of 80 participants (40 with depression and 40 normal control) showed that when only one question (Q1) of "How are you these days?" was used, the recall, precision, specificity, and accuracy were 82.5%, 84.65, 85.00, and 83.75%, respectively. When utilizing the first three questions from Thai depression assessment tasks (Q1 - Q3), the values increased to 87.50%, 92.11%, 92.50%, and 90.00%, respectively. The local interpretable model explanations were analyzed to determine which words contributed the most to the model's word cloud visualization. Our findings were consistent with previously published literature and provide similar explanation for clinical settings. It was discovered that the classification model for individuals with depression relied heavily on negative terms such as 'not,' 'sad,', 'mood', 'suicide', 'bad', and 'bore' whereas normal control participants used neutral to positive terms such as 'recently,' 'fine,', 'normally', 'work', and 'working'. The findings of the study suggest that screening for depression can be facilitated by eliciting just three questions from patients with depression, making the process more accessible and less time-consuming while reducing the already huge burden on healthcare workers.

With the advent of Neural Networks, Neural Machine Translation (NMT) has been a booming area of research in Natural Language Processing. Indic languages possess less significant parallel and monolingual corpus than English and other European languages. Even in Indic languages, many Indo-Aryan and Dravidian languages fall into low-resource languages, and techniques like Back Translation, Unsupervised Neural Machine Translation (UNMT), and Transfer Learning help achieve better translation accuracy. This paper uses the UNMT approach with a pre-trained Cross-Lingual Language Model (XLM) for the English to Kannada language pair. Our proposed methodology has achieved a 0.61 BLEU score in English to Kannada and a 0.32 BLEU score in Kannada to English translation.