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Reasoning-oriented large language models (RLMs) achieve strong gains on tasks such as mathematics and coding by generating explicit intermediate reasoning. However, their impact on machine translation (MT) remains underexplored. We…

Computation and Language · Computer Science 2026-02-17 Sara Rajaee , Sebastian Vincent , Alexandre Berard , Marzieh Fadaee , Kelly Marchisio , Tom Kocmi

Large Language Models (LLMs) demonstrate remarkable capabilities in replicating human tasks and boosting productivity. However, their direct application for data extraction presents limitations due to a prioritisation of fluency over…

Computation and Language · Computer Science 2024-06-13 Aman Ahluwalia , Suhrud Wani

Large language models applied to vast biological datasets have the potential to transform biology by uncovering disease mechanisms and accelerating drug development. However, current models are often siloed, trained separately on…

Large Language Models (LLMs) stand at the forefront of a number of Natural Language Processing (NLP) tasks. Despite the widespread adoption of LLMs in NLP, much of their potential in broader fields remains largely unexplored, and…

Machine Learning · Computer Science 2024-03-11 Zhiqiang Zhong , Kuangyu Zhou , Davide Mottin

Biological sequences encode fundamental instructions for the building blocks of life, in the form of DNA, RNA, and proteins. Modeling these sequences is key to understand disease mechanisms and is an active research area in computational…

Large language models (LLMs) are a class of artificial intelligence models based on deep learning, which have great performance in various tasks, especially in natural language processing (NLP). Large language models typically consist of…

Quantitative Methods · Quantitative Biology 2025-02-04 Jiajia Liu , Mengyuan Yang , Yankai Yu , Haixia Xu , Tiangang Wang , Kang Li , Xiaobo Zhou

RNA plays a pivotal role in translating genetic instructions into functional outcomes, underscoring its importance in biological processes and disease mechanisms. Despite the emergence of numerous deep learning approaches for RNA,…

Quantitative Methods · Quantitative Biology 2024-12-13 Yuchen Ren , Zhiyuan Chen , Lifeng Qiao , Hongtai Jing , Yuchen Cai , Sheng Xu , Peng Ye , Xinzhu Ma , Siqi Sun , Hongliang Yan , Dong Yuan , Wanli Ouyang , Xihui Liu

Large Language models (LLMs) have emerged as powerful tools for addressing challenges across diverse domains. Notably, recent studies have demonstrated that large language models significantly enhance the efficiency of biomolecular analysis…

Computation and Language · Computer Science 2025-03-07 Jiyue Jiang , Zikang Wang , Yuheng Shan , Heyan Chai , Jiayi Li , Zixian Ma , Xinrui Zhang , Yu Li

RNA, whose functionality is largely determined by its structure, plays an important role in many biological activities. The prediction of pairwise structural proximity between each nucleotide of an RNA sequence can characterize the…

Quantitative Methods · Quantitative Biology 2024-01-22 Yiren Jian , Chongyang Gao , Chen Zeng , Yunjie Zhao , Soroush Vosoughi

Despite the inherent limitations of existing Large Language Models in directly reading and interpreting single-cell omics data, they demonstrate significant potential and flexibility as the Foundation Model. This research focuses on how to…

Genomics · Quantitative Biology 2024-02-21 Cong Li , Meng Xiao , Pengfei Wang , Guihai Feng , Xin Li , Yuanchun Zhou

The development of Large Speech-Language Models (LSLMs) has been slowed by fragmented architectures and a lack of transparency, hindering the systematic comparison and reproducibility of research. Unlike in the vision-language domain, the…

Computation and Language · Computer Science 2025-08-22 Yirong Sun , Yizhong Geng , Peidong Wei , Yanjun Chen , Jinghan Yang , Rongfei Chen , Wei Zhang , Xiaoyu Shen

Large Language Models (LLMs) have substantially driven scientific progress in various domains, and many papers have demonstrated their ability to tackle complex problems with creative solutions. Our paper introduces a new foundation model,…

Large language models (LLMs) often struggle to perform multi-target reasoning in long-context scenarios where relevant information is scattered across extensive documents. To address this challenge, we introduce NeuroSymbolic Augmented…

Computation and Language · Computer Science 2025-06-04 Sina Bagheri Nezhad , Ameeta Agrawal

Recent advances in Multimodal Large Language Models (MLLMs) have shown remarkable capabilities in understanding both images and 3D data, yet these modalities face inherent limitations in comprehensively representing object geometry and…

Computer Vision and Pattern Recognition · Computer Science 2025-04-22 Andrea Amaduzzi , Pierluigi Zama Ramirez , Giuseppe Lisanti , Samuele Salti , Luigi Di Stefano

Protein language models are a powerful tool for learning protein representations through pre-training on vast protein sequence datasets. However, traditional protein language models lack explicit structural supervision, despite its…

Biomolecules · Quantitative Biology 2024-02-09 Zuobai Zhang , Jiarui Lu , Vijil Chenthamarakshan , Aurélie Lozano , Payel Das , Jian Tang

Deciphering the function of unseen protein sequences is a fundamental challenge with broad scientific impact, yet most existing methods depend on task-specific adapters or large-scale supervised fine-tuning. We introduce the…

Machine Learning · Computer Science 2025-10-14 Xinhui Chen , Zuchao Li , Mengqi Gao , Yufeng Zhang , Chak Tou Leong , Haoyang Li , Jiaqi Chen

Large language models (LLMs) have significantly advanced natural language processing, excelling in areas like text generation, summarization, and question-answering. Despite their capabilities, these models face challenges when fine-tuned…

Computation and Language · Computer Science 2024-12-23 Ali Hamdi , Hozaifa Kassab , Mohamed Bahaa , Marwa Mohamed

We present MiMo-7B, a large language model born for reasoning tasks, with optimization across both pre-training and post-training stages. During pre-training, we enhance the data preprocessing pipeline and employ a three-stage data mixing…

This paper demonstrates that language models are strong structure-based protein designers. We present LM-Design, a generic approach to reprogramming sequence-based protein language models (pLMs), that have learned massive sequential…

Machine Learning · Computer Science 2023-02-10 Zaixiang Zheng , Yifan Deng , Dongyu Xue , Yi Zhou , Fei YE , Quanquan Gu

Large Language Models (LLMs) represent a class of deep learning models adept at understanding natural language and generating coherent responses to various prompts or queries. These models far exceed the complexity of conventional neural…

Machine Learning · Computer Science 2024-12-05 Minghao Shao , Abdul Basit , Ramesh Karri , Muhammad Shafique