Detecting protein-protein interactions (PPIs) is crucial for understanding genetic mechanisms, disease pathogenesis, and drug design. However, with the fast-paced growth of biomedical literature, there is a growing need for automated and accurate extraction of PPIs to facilitate scientific knowledge discovery. Pre-trained language models, such as generative pre-trained transformer (GPT) and bidirectional encoder representations from transformers (BERT), have shown promising results in natural language processing (NLP) tasks. We evaluated the PPI identification performance of various GPT and BERT models using a manually curated benchmark corpus of 164 PPIs in 77 sentences from learning language in logic (LLL). BERT-based models achieved the best overall performance, with PubMedBERT achieving the highest precision (85.17%) and F1-score (86.47%) and BioM-ALBERT achieving the highest recall (93.83%). Despite not being explicitly trained for biomedical texts, GPT-4 achieved comparable performance to the best BERT models with 83.34% precision, 76.57% recall, and 79.18% F1-score. These findings suggest that GPT models can effectively detect PPIs from text data and have the potential for use in biomedical literature mining tasks.
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Recent advances in large language models have enabled them to reach a level of text generation comparable to that of humans. These models show powerful capabilities across a wide range of content, including news article writing, story generation, and scientific writing. Such capability further narrows the gap between human-authored and machine-generated texts, highlighting the importance of deepfake text detection to avoid potential risks such as fake news propagation and plagiarism. However, previous work has been limited in that they testify methods on testbed of specific domains or certain language models. In practical scenarios, the detector faces texts from various domains or LLMs without knowing their sources. To this end, we build a wild testbed by gathering texts from various human writings and deepfake texts generated by different LLMs. Human annotators are only slightly better than random guessing at identifying machine-generated texts. Empirical results on automatic detection methods further showcase the challenges of deepfake text detection in a wild testbed. In addition, out-of-distribution poses a greater challenge for a detector to be employed in realistic application scenarios. We release our resources at //github.com/yafuly/DeepfakeTextDetect.
Automated stance detection and related machine learning methods can provide useful insights for media monitoring and academic research. Many of these approaches require annotated training datasets, which limits their applicability for languages where these may not be readily available. This paper explores the applicability of large language models for automated stance detection in a challenging scenario, involving a morphologically complex, lower-resource language, and a socio-culturally complex topic, immigration. If the approach works in this case, it can be expected to perform as well or better in less demanding scenarios. We annotate a large set of pro and anti-immigration examples, and compare the performance of multiple language models as supervised learners. We also probe the usability of ChatGPT as an instructable zero-shot classifier for the same task. Supervised achieves acceptable performance, and ChatGPT yields similar accuracy. This is promising as a potentially simpler and cheaper alternative for text classification tasks, including in lower-resource languages. We further use the best-performing model to investigate diachronic trends over seven years in two corpora of Estonian mainstream and right-wing populist news sources, demonstrating the applicability of the approach for news analytics and media monitoring settings, and discuss correspondences between stance changes and real-world events.
This research study investigates the efficiency of different information retrieval (IR) systems in accessing relevant information from the scientific literature during the COVID-19 pandemic. The study applies the TREC framework to the COVID-19 Open Research Dataset (CORD-19) and evaluates BM25, Contriever, and Bag of Embeddings IR frameworks. The objective is to build a test collection for search engines that tackle the complex information landscape during a pandemic. The study uses the CORD-19 dataset to train and evaluate the IR models and compares the results to those manually labeled in the TREC-COVID IR Challenge. The results indicate that advanced IR models like BERT and Contriever better retrieve relevant information during a pandemic. However, the study also highlights the challenges in processing large datasets and the need for strategies to focus on abstracts or summaries. Overall, the research highlights the importance of effectively tailored IR systems in dealing with information overload during crises like COVID-19 and can guide future research and development in this field.
With contrastive pre-training, sentence encoders are generally optimized to locate semantically similar samples closer to each other in their embedding spaces. In this work, we focus on the potential of their embedding spaces to be readily adapted to zero-shot text classification, as semantically distinct samples are already well-separated. Our framework, RaLP (Retrieval augmented Label Prompts for sentence encoder), encodes prompted label candidates with a sentence encoder, then assigns the label whose prompt embedding has the highest similarity with the input text embedding. In order to compensate for the potentially poorly descriptive labels in their original format, RaLP retrieves sentences that are semantically similar to the original label prompt from external corpora and use them as additional pseudo-label prompts. RaLP achieves competitive or stronger performance than much larger baselines on various closed-set classification and multiple-choice QA datasets under zero-shot settings. We show that the retrieval component plays a pivotal role in RaLP's success, and its results are robustly attained regardless of verbalizer variations.
In traditional machine learning, it is trivial to conduct model evaluation since all data samples are managed centrally by a server. However, model evaluation becomes a challenging problem in federated learning (FL), which is called federated evaluation in this work. This is because clients do not expose their original data to preserve data privacy. Federated evaluation plays a vital role in client selection, incentive mechanism design, malicious attack detection, etc. In this paper, we provide the first comprehensive survey of existing federated evaluation methods. Moreover, we explore various applications of federated evaluation for enhancing FL performance and finally present future research directions by envisioning some challenges.
Time-Series Mining (TSM) is an important research area since it shows great potential in practical applications. Deep learning models that rely on massive labeled data have been utilized for TSM successfully. However, constructing a large-scale well-labeled dataset is difficult due to data annotation costs. Recently, Pre-Trained Models have gradually attracted attention in the time series domain due to their remarkable performance in computer vision and natural language processing. In this survey, we provide a comprehensive review of Time-Series Pre-Trained Models (TS-PTMs), aiming to guide the understanding, applying, and studying TS-PTMs. Specifically, we first briefly introduce the typical deep learning models employed in TSM. Then, we give an overview of TS-PTMs according to the pre-training techniques. The main categories we explore include supervised, unsupervised, and self-supervised TS-PTMs. Further, extensive experiments are conducted to analyze the advantages and disadvantages of transfer learning strategies, Transformer-based models, and representative TS-PTMs. Finally, we point out some potential directions of TS-PTMs for future work.
Generating free-text rationales is a promising step towards explainable NLP, yet evaluating such rationales remains a challenge. Existing metrics have mostly focused on measuring the association between the rationale and a given label. We argue that an ideal metric should focus on the new information uniquely provided in the rationale that is otherwise not provided in the input or the label. We investigate this research problem from an information-theoretic perspective using conditional V-information (Hewitt et al., 2021). More concretely, we propose a metric called REV (Rationale Evaluation with conditional V-information), to quantify the amount of new, label-relevant information in a rationale beyond the information already available in the input or the label. Experiments across four benchmarks with reasoning tasks, including chain-of-thought, demonstrate the effectiveness of REV in evaluating rationale-label pairs, compared to existing metrics. We further demonstrate REV is consistent with human judgments on rationale evaluations and provides more sensitive measurements of new information in free-text rationales. When used alongside traditional performance metrics, REV provides deeper insights into models' reasoning and prediction processes.
Following unprecedented success on the natural language tasks, Transformers have been successfully applied to several computer vision problems, achieving state-of-the-art results and prompting researchers to reconsider the supremacy of convolutional neural networks (CNNs) as {de facto} operators. Capitalizing on these advances in computer vision, the medical imaging field has also witnessed growing interest for Transformers that can capture global context compared to CNNs with local receptive fields. Inspired from this transition, in this survey, we attempt to provide a comprehensive review of the applications of Transformers in medical imaging covering various aspects, ranging from recently proposed architectural designs to unsolved issues. Specifically, we survey the use of Transformers in medical image segmentation, detection, classification, reconstruction, synthesis, registration, clinical report generation, and other tasks. In particular, for each of these applications, we develop taxonomy, identify application-specific challenges as well as provide insights to solve them, and highlight recent trends. Further, we provide a critical discussion of the field's current state as a whole, including the identification of key challenges, open problems, and outlining promising future directions. We hope this survey will ignite further interest in the community and provide researchers with an up-to-date reference regarding applications of Transformer models in medical imaging. Finally, to cope with the rapid development in this field, we intend to regularly update the relevant latest papers and their open-source implementations at \url{//github.com/fahadshamshad/awesome-transformers-in-medical-imaging}.
Transformer-based pretrained language models (T-PTLMs) have achieved great success in almost every NLP task. The evolution of these models started with GPT and BERT. These models are built on the top of transformers, self-supervised learning and transfer learning. Transformed-based PTLMs learn universal language representations from large volumes of text data using self-supervised learning and transfer this knowledge to downstream tasks. These models provide good background knowledge to downstream tasks which avoids training of downstream models from scratch. In this comprehensive survey paper, we initially give a brief overview of self-supervised learning. Next, we explain various core concepts like pretraining, pretraining methods, pretraining tasks, embeddings and downstream adaptation methods. Next, we present a new taxonomy of T-PTLMs and then give brief overview of various benchmarks including both intrinsic and extrinsic. We present a summary of various useful libraries to work with T-PTLMs. Finally, we highlight some of the future research directions which will further improve these models. We strongly believe that this comprehensive survey paper will serve as a good reference to learn the core concepts as well as to stay updated with the recent happenings in T-PTLMs.
This paper surveys and organizes research works in a new paradigm in natural language processing, which we dub "prompt-based learning". Unlike traditional supervised learning, which trains a model to take in an input x and predict an output y as P(y|x), prompt-based learning is based on language models that model the probability of text directly. To use these models to perform prediction tasks, the original input x is modified using a template into a textual string prompt x' that has some unfilled slots, and then the language model is used to probabilistically fill the unfilled information to obtain a final string x, from which the final output y can be derived. This framework is powerful and attractive for a number of reasons: it allows the language model to be pre-trained on massive amounts of raw text, and by defining a new prompting function the model is able to perform few-shot or even zero-shot learning, adapting to new scenarios with few or no labeled data. In this paper we introduce the basics of this promising paradigm, describe a unified set of mathematical notations that can cover a wide variety of existing work, and organize existing work along several dimensions, e.g.the choice of pre-trained models, prompts, and tuning strategies. To make the field more accessible to interested beginners, we not only make a systematic review of existing works and a highly structured typology of prompt-based concepts, but also release other resources, e.g., a website //pretrain.nlpedia.ai/ including constantly-updated survey, and paperlist.
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