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In the realm of natural language processing, the understanding of tabular data has perpetually stood as a focal point of scholarly inquiry. The emergence of expansive language models, exemplified by the likes of ChatGPT, has ushered in a…

Computation and Language · Computer Science 2023-08-29 Hengyuan Zhang , Peng Chang , Zongcheng Ji

Over the last few years, large language models (LLMs) have emerged as the most important breakthroughs in natural language processing (NLP) that fundamentally transform research and developments in the field. ChatGPT represents one of the…

Computation and Language · Computer Science 2023-04-13 Viet Dac Lai , Nghia Trung Ngo , Amir Pouran Ben Veyseh , Hieu Man , Franck Dernoncourt , Trung Bui , Thien Huu Nguyen

The development of single-cell and spatial transcriptomics has revolutionized our capacity to investigate cellular properties, functions, and interactions in both cellular and spatial contexts. However, the analysis of single-cell and…

Genomics · Quantitative Biology 2024-12-09 Shuang Ge , Shuqing Sun , Huan Xu , Qiang Cheng , Zhixiang Ren

Scientific articles play a crucial role in advancing knowledge and informing research directions. One key aspect of evaluating scientific articles is the analysis of citations, which provides insights into the impact and reception of the…

Digital Libraries · Computer Science 2026-03-09 Walid Hariri

With the surge of ChatGPT,the use of large models has significantly increased,rapidly rising to prominence across the industry and sweeping across the internet. This article is a comprehensive review of fine-tuning methods for large models.…

Machine Learning · Computer Science 2024-04-16 Benjue Weng

Recent advancements in specialized large-scale architectures for training image and language have profoundly impacted the field of computer vision and natural language processing (NLP). Language models, such as the recent ChatGPT and GPT4…

Biomolecules · Quantitative Biology 2023-05-04 Sergio Romero-Romero , Sebastian Lindner , Noelia Ferruz

ChatGPT has drawn considerable attention from both the general public and domain experts with its remarkable text generation capabilities. This has subsequently led to the emergence of diverse applications in the field of biomedicine and…

This dissertation explores the application of machine learning in molecular biology, focusing on gene expression regulation and cellular behavior at the single-cell level. Using modern neural networks, the research addresses key challenges…

Quantitative Methods · Quantitative Biology 2024-10-01 Yongjian Yang

Cell type annotation is a fundamental step in the analysis of single-cell RNA sequencing (scRNA-seq) data. In practice, human experts often rely on the structure revealed by principal component analysis (PCA) followed by $k$-nearest…

Genomics · Quantitative Biology 2026-02-10 Tianxiang Hu , Chenyi Zhou , Jiaxiang Liu , Jiongxin Wang , Ruizhe Chen , Haoxiang Xia , Gaoang Wang , Jian Wu , Zuozhu Liu

Single-cell reference atlases are large-scale, cell-level maps that capture cellular heterogeneity within an organ using single cell genomics. Given their size and cellular diversity, these atlases serve as high-quality training data for…

Genomics · Quantitative Biology 2022-11-09 Jan Engelmann , Leon Hetzel , Giovanni Palla , Lisa Sikkema , Malte Luecken , Fabian Theis

Harnessing the potential of large language models (LLMs) like ChatGPT can help address social challenges through inclusive, ethical, and sustainable means. In this paper, we investigate the extent to which ChatGPT can annotate data for…

Artificial Intelligence · Computer Science 2024-07-10 Yiming Zhu , Peixian Zhang , Ehsan-Ul Haq , Pan Hui , Gareth Tyson

Large Language Models (LLMs), such as ChatGPT, are reshaping content creation and academic writing. This study investigates the impact of AI-assisted generative revisions on research manuscripts, focusing on heterogeneous adoption patterns…

Computation and Language · Computer Science 2025-04-21 Cong William Lin , Wu Zhu

Large language models, such as the well-known ChatGPT, have brought about an unexpected revolution in the field of artificial intelligence. On the one hand, they have numerous practical applications and enormous potential still to be…

Computation and Language · Computer Science 2025-02-26 Carlos Gómez-Rodríguez

Text data augmentation is an effective strategy for overcoming the challenge of limited sample sizes in many natural language processing (NLP) tasks. This challenge is especially prominent in the few-shot learning scenario, where the data…

Large Language Models (LLMs) have revolutionized various sectors, including healthcare where they are employed in diverse applications. Their utility is particularly significant in the context of rare diseases, where data scarcity,…

Computation and Language · Computer Science 2024-08-20 Qiuhao Lu , Rui Li , Andrew Wen , Jinlian Wang , Liwei Wang , Hongfang Liu

Since the launch of ChatGPT in late 2022, the capacities of Large Language Models and their evaluation have been in constant discussion and evaluation both in academic research and in the industry. Scenarios and benchmarks have been…

Computation and Language · Computer Science 2025-04-04 Subramaniam Vincent , Phoebe Wang , Zhan Shi , Sahas Koka , Yi Fang

With ongoing developments and innovations in single-cell RNA sequencing methods, advancements in sequencing performance could empower significant discoveries as well as new emerging possibilities to address biological and medical…

Applications · Statistics 2019-12-19 Jiawei Long , Yu Xia

In recent years, the field of single-cell data analysis has seen a marked advancement in the development of clustering methods. Despite advancements, most of these algorithms still concentrate on analyzing the provided single-cell matrix…

Machine Learning · Computer Science 2023-12-18 Dayu Hu , Ke Liang , Hao Yu , Xinwang Liu

Massive single-cell profiling efforts have accelerated our discovery of the cellular composition of the human body, while at the same time raising the need to formalise this new knowledge. Here, we review current cell ontology efforts to…

Cell Behavior · Quantitative Biology 2021-11-10 David Osumi-Sutherland , Chuan Xu , Maria Keays , Peter V. Kharchenko , Aviv Regev , Ed Lein , Sarah A. Teichmann

This paper assesses the accuracy, reliability and bias of the Large Language Model (LLM) ChatGPT-4 on the text analysis task of classifying the political affiliation of a Twitter poster based on the content of a tweet. The LLM is compared…

Computation and Language · Computer Science 2023-04-14 Petter Törnberg