English
Related papers

Related papers: Rethinking Text-based Protein Understanding: Retri…

200 papers

As Large Language Models (LLMs) become increasingly prevalent, their generated outputs are proliferating across the web, risking a future where machine-generated content dilutes human-authored text. Since online data is the primary resource…

Computation and Language · Computer Science 2025-09-23 George Drayson , Emine Yilmaz , Vasileios Lampos

Natural language processing (NLP) has significantly influenced scientific domains beyond human language, including protein engineering, where pre-trained protein language models (PLMs) have demonstrated remarkable success. However,…

Computation and Language · Computer Science 2025-03-20 Yang Tan , Chen Liu , Jingyuan Gao , Banghao Wu , Mingchen Li , Ruilin Wang , Lingrong Zhang , Huiqun Yu , Guisheng Fan , Liang Hong , Bingxin Zhou

Text generation has become one of the most important yet challenging tasks in natural language processing (NLP). The resurgence of deep learning has greatly advanced this field by neural generation models, especially the paradigm of…

Computation and Language · Computer Science 2021-05-26 Junyi Li , Tianyi Tang , Wayne Xin Zhao , Ji-Rong Wen

Large Language Models (LLMs) have the unique capability to understand and generate human-like text from input queries. When fine-tuned, these models show enhanced performance on domain-specific queries. OpenAI highlights the process of…

Computation and Language · Computer Science 2024-07-02 Scott Barnett , Zac Brannelly , Stefanus Kurniawan , Sheng Wong

Large Language Models (LLMs) have shown strong capabilities in document re-ranking, a key component in modern Information Retrieval (IR) systems. However, existing LLM-based approaches face notable limitations, including ranking…

Information Retrieval · Computer Science 2025-10-03 Pinhuan Wang , Zhiqiu Xia , Chunhua Liao , Feiyi Wang , Hang Liu

Recent studies have proposed leveraging Large Language Models (LLMs) as information retrievers through query rewriting. However, for challenging corpora, we argue that enhancing queries alone is insufficient for robust semantic matching;…

Information Retrieval · Computer Science 2025-06-24 Jingming Liu , Yumeng Li , Wei Shi , Yao-Xiang Ding , Hui Su , Kun Zhou

We present a new approach for benchmarking Large Language Model (LLM) capabilities on research-level mathematics. Existing benchmarks largely rely on static, hand-curated sets of contest or textbook-style problems as proxies for…

Artificial Intelligence · Computer Science 2026-03-02 Antoine Peyronnet , Fabian Gloeckle , Amaury Hayat

The prediction of protein structures from sequences is an important task for function prediction, drug design, and related biological processes understanding. Recent advances have proved the power of language models (LMs) in processing the…

Quantitative Methods · Quantitative Biology 2022-12-01 Bozhen Hu , Jun Xia , Jiangbin Zheng , Cheng Tan , Yufei Huang , Yongjie Xu , Stan Z. Li

Large language models (LLMs) present significant risks when used to generate non-factual content and spread disinformation at scale. Detecting such LLM-generated content is crucial, yet current detectors often struggle to generalize in…

Computation and Language · Computer Science 2025-02-18 Ran Li , Wei Hao , Weiliang Zhao , Junfeng Yang , Chengzhi Mao

This paper proposes LayoutLLM, a more flexible document analysis method for understanding imaged documents. Visually Rich Document Understanding tasks, such as document image classification and information extraction, have gained…

Computation and Language · Computer Science 2024-03-22 Masato Fujitake

The increasing use of text as data in social science research necessitates the development of valid, consistent, reproducible, and efficient methods for generating text-based concept measures. This paper presents a novel method that…

Computation and Language · Computer Science 2024-09-20 Yi Yang , Hanyu Duan , Jiaxin Liu , Kar Yan Tam

Large Language Models (LLMs) are now widely used for query reformulation and expansion in Information Retrieval, with many studies reporting substantial effectiveness gains. However, these results are typically obtained under heterogeneous…

Information Retrieval · Computer Science 2026-05-01 Amin Bigdeli , Radin Hamidi Rad , Hai Son Le , Mert Incesu , Negar Arabzadeh , Charles L. A. Clarke , Ebrahim Bagheri

Automatic relationship extraction (RE) from biomedical literature is critical for managing the vast amount of scientific knowledge produced each year. In recent years, utilizing pre-trained language models (PLMs) has become the prevalent…

Computation and Language · Computer Science 2025-11-04 Mario Sänger , Ulf Leser

Protein language models have shown remarkable success in learning biological information from protein sequences. However, most existing models are limited by either autoencoding or autoregressive pre-training objectives, which makes them…

Quantitative Methods · Quantitative Biology 2024-12-10 Bo Chen , Xingyi Cheng , Pan Li , Yangli-ao Geng , Jing Gong , Shen Li , Zhilei Bei , Xu Tan , Boyan Wang , Xin Zeng , Chiming Liu , Aohan Zeng , Yuxiao Dong , Jie Tang , Le Song

Recent large language models (LLM) are leveraging human feedback to improve their generation quality. However, human feedback is costly to obtain, especially during inference. In this work, we propose LLMRefine, an inference time…

Computation and Language · Computer Science 2024-10-28 Wenda Xu , Daniel Deutsch , Mara Finkelstein , Juraj Juraska , Biao Zhang , Zhongtao Liu , William Yang Wang , Lei Li , Markus Freitag

Large language models (LLMs) are becoming useful in many domains due to their impressive abilities that arise from large training datasets and large model sizes. However, research on LLM-based approaches to document inconsistency detection…

Computation and Language · Computer Science 2026-04-09 Nelvin Tan , Yaowen Zhang , James Asikin Cheung , Fusheng Liu , Yu-Ching Shih , Dong Yang

We introduce a simple approach that uses a large language model (LLM) to automatically implement a fully interpretable rule-based data-to-text system in pure Python. Experimental evaluation on the WebNLG dataset showed that such a…

Computation and Language · Computer Science 2025-03-03 Jędrzej Warczyński , Mateusz Lango , Ondrej Dusek

Reranking is fundamental to information retrieval and retrieval-augmented generation, with recent Large Language Models (LLMs) significantly advancing reranking quality. Most current works rely on large-scale LLMs (>7B parameters),…

Information Retrieval · Computer Science 2026-04-17 Xianming Li , Aamir Shakir , Rui Huang , Tsz-fung Andrew Lee , Julius Lipp , Benjamin Clavié , Jing Li

High-quality training data has proven crucial for developing performant large language models (LLMs). However, commercial LLM providers disclose few, if any, details about the data used for training. This lack of transparency creates…

We explore optimally training protein language models, an area of significant interest in biological research where guidance on best practices is limited. Most models are trained with extensive compute resources until performance gains…

Machine Learning · Computer Science 2024-11-05 Xingyi Cheng , Bo Chen , Pan Li , Jing Gong , Jie Tang , Le Song
‹ Prev 1 3 4 5 6 7 10 Next ›