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Recent advancements in deep learning, particularly large language models (LLMs), made a significant impact on how researchers study microbiome and metagenomics data. Microbial protein and genomic sequences, like natural languages, form a…

Quantitative Methods · Quantitative Biology 2024-09-18 Binghao Yan , Yunbi Nam , Lingyao Li , Rebecca A. Deek , Hongzhe Li , Siyuan Ma

Large language models (LLMs) are a special class of pretrained language models obtained by scaling model size, pretraining corpus and computation. LLMs, because of their large size and pretraining on large volumes of text data, exhibit…

Computation and Language · Computer Science 2023-10-20 Katikapalli Subramanyam Kalyan

Large language models (LLMs) exhibit cultural bias from overrepresented viewpoints in training data, yet cultural alignment remains a challenge due to limited cultural knowledge and a lack of exploration into effective learning approaches.…

Computation and Language · Computer Science 2025-12-16 Chunhua Liu , Kabir Manandhar Shrestha , Sukai Huang

This paper discusses the methods that we used for our submissions to the WMT 2023 Terminology Shared Task for German-to-English (DE-EN), English-to-Czech (EN-CS), and Chinese-to-English (ZH-EN) language pairs. The task aims to advance…

Computation and Language · Computer Science 2025-03-04 Yasmin Moslem , Gianfranco Romani , Mahdi Molaei , Rejwanul Haque , John D. Kelleher , Andy Way

In model-driven engineering, metamodel evolution leads to the need to adapt corresponding grammars to maintain consistency, which typically requires tedious manual work. Existing rule-based methods can achieve partial automation but have…

Computation and Language · Computer Science 2026-05-21 Weixing Zhang , Bowen Jiang , Rahul Sharma , Regina Hebig , Daniel Strüber

Large Language Models (LLMs) have emerged as a transformative power in enhancing natural language comprehension, representing a significant stride toward artificial general intelligence. The application of LLMs extends beyond conventional…

Purpose: Large Language Models (LLMs) like GPT (Generative Pre-trained Transformer) from OpenAI and LLaMA (Large Language Model Meta AI) from Meta AI are increasingly recognized for their potential in the field of cheminformatics,…

Biomolecules · Quantitative Biology 2024-05-22 Shaghayegh Sadeghi , Alan Bui , Ali Forooghi , Jianguo Lu , Alioune Ngom

Background: Identification of the interactions and regulatory relations between biomolecules play pivotal roles in understanding complex biological systems and the mechanisms underlying diverse biological functions. However, the collection…

Computation and Language · Computer Science 2025-04-24 Gilchan Park , Byung-Jun Yoon , Xihaier Luo , Vanessa López-Marrero , Shinjae Yoo , Shantenu Jha

Artificial intelligence (AI) is widely deployed to solve problems related to marketing attribution and budget optimization. However, AI models can be quite complex, and it can be difficult to understand model workings and insights without…

Computation and Language · Computer Science 2024-04-23 Yilin Gao , Sai Kumar Arava , Yancheng Li , James W. Snyder

Data science plays a critical role in biomedical research, but it requires professionals with expertise in coding and medical data analysis. Large language models (LLMs) have shown great potential in supporting medical tasks and performing…

Artificial Intelligence · Computer Science 2025-04-10 Zifeng Wang , Benjamin Danek , Ziwei Yang , Zheng Chen , Jimeng Sun

In recent years, protein-text models have gained significant attention for their potential in protein generation and understanding. Current approaches focus on integrating protein-related knowledge into large language models through…

Computation and Language · Computer Science 2025-11-11 Juntong Wu , Zijing Liu , He Cao , Hao Li , Bin Feng , Zishan Shu , Ke Yu , Li Yuan , Yu Li

Large Language Models (LLM) have made significant advances in the recent past becoming more mainstream in Artificial Intelligence (AI) enabled human-facing applications. However, LLMs often generate stereotypical output inherited from…

Computation and Language · Computer Science 2023-11-27 Wu Zekun , Sahan Bulathwela , Adriano Soares Koshiyama

Large language models (LLMs) are a promising venue for natural language understanding and generation. However, current LLMs are far from reliable: they are prone to generating non-factual information and, more crucially, to contradicting…

Computation and Language · Computer Science 2024-09-24 Diego Calanzone , Stefano Teso , Antonio Vergari

Large language models (LLMs) are introducing a paradigm shift in molecular discovery by enabling text-guided interaction with chemical spaces through natural language, symbolic notations, with emerging extensions to incorporate multi-modal…

Machine Learning · Computer Science 2025-05-23 Ziqing Wang , Kexin Zhang , Zihan Zhao , Yibo Wen , Abhishek Pandey , Han Liu , Kaize Ding

Large language models (LLMs) have emerged as powerful tools for medical information retrieval, yet their accuracy and depth remain limited in specialized domains such as Alzheimer's disease (AD), a growing global health challenge. To…

Large language models (LLMs) have notably enhanced the fluency and diversity of machine-generated text. However, this progress also presents a significant challenge in detecting the origin of a given text, and current research on detection…

Computation and Language · Computer Science 2023-10-05 Xianjun Yang , Wei Cheng , Yue Wu , Linda Petzold , William Yang Wang , Haifeng Chen

The paradigm of large language models in natural language processing (NLP) has also shown promise in modeling biological languages, including proteins, RNA, and DNA. Both the auto-regressive generation paradigm and evaluation metrics have…

Biomolecules · Quantitative Biology 2025-07-04 Ke Liu , Shuaike Shen , Hao Chen

Recent advancements in the field of Natural Language Processing, particularly the development of large-scale language models that are pretrained on vast amounts of knowledge, are creating novel opportunities within the realm of Knowledge…

Computation and Language · Computer Science 2023-10-06 Anisa Rula , Jennifer D'Souza

As content generated by Large Language Model (LLM) has grown exponentially, the ability to accurately identify and fingerprint such text has become increasingly crucial. In this work, we introduce a novel black-box approach for…

Cryptography and Security · Computer Science 2024-08-07 Dmitri Iourovitski , Sanat Sharma , Rakshak Talwar

In the fast-evolving domain of artificial intelligence, large language models (LLMs) such as GPT-3 and GPT-4 are revolutionizing the landscapes of finance, healthcare, and law: domains characterized by their reliance on professional…

Computation and Language · Computer Science 2024-11-25 Zhiyu Zoey Chen , Jing Ma , Xinlu Zhang , Nan Hao , An Yan , Armineh Nourbakhsh , Xianjun Yang , Julian McAuley , Linda Petzold , William Yang Wang