English
Related papers

Related papers: InstructProtein: Aligning Human and Protein Langua…

200 papers

Large Language Models (LLMs) have exhibited impressive proficiency in various natural language processing (NLP) tasks, which involve increasingly complex reasoning. Knowledge reasoning, a primary type of reasoning, aims at deriving new…

Computation and Language · Computer Science 2024-07-02 Yifei Zhang , Xintao Wang , Jiaqing Liang , Sirui Xia , Lida Chen , Yanghua Xiao

Instruction tuning is a supervised fine-tuning approach that significantly improves the ability of large language models (LLMs) to follow human instructions. We propose SelfCodeAlign, the first fully transparent and permissive pipeline for…

Computation and Language · Computer Science 2024-11-04 Yuxiang Wei , Federico Cassano , Jiawei Liu , Yifeng Ding , Naman Jain , Zachary Mueller , Harm de Vries , Leandro von Werra , Arjun Guha , Lingming Zhang

Protein representation learning is critical for numerous biological tasks. Recently, large transformer-based protein language models (pLMs) pretrained on large scale protein sequences have demonstrated significant success in sequence-based…

Machine Learning · Computer Science 2025-08-12 Xuefeng Liu , Songhao Jiang , Chih-chan Tien , Jinbo Xu , Rick Stevens

Proteins are fundamental components of biological systems and can be represented through various modalities, including sequences, structures, and textual descriptions. Despite the advances in deep learning and scientific large language…

Machine Learning · Computer Science 2024-07-15 Zhiyuan Chen , Tianhao Chen , Chenggang Xie , Yang Xue , Xiaonan Zhang , Jingbo Zhou , Xiaomin Fang

Recent studies customizing Multimodal Large Language Models (MLLMs) for domain-specific tasks have yielded promising results, especially in the field of scientific chart comprehension. These studies generally utilize visual instruction…

Computer Vision and Pattern Recognition · Computer Science 2025-07-21 Wan-Cyuan Fan , Yen-Chun Chen , Mengchen Liu , Lu Yuan , Leonid Sigal

In recent years, significant progress has been made in the field of protein function prediction with the development of various machine-learning approaches. However, most existing methods formulate the task as a multi-classification…

Quantitative Methods · Quantitative Biology 2024-04-23 Hadi Abdine , Michail Chatzianastasis , Costas Bouyioukos , Michalis Vazirgiannis

Instruction tuning enhances large language models (LLMs) to follow human instructions across diverse tasks, relying on high-quality datasets to guide behavior. However, these datasets, whether manually curated or synthetically generated,…

Machine learning practitioners often face significant challenges in formally integrating their prior knowledge and beliefs into predictive models, limiting the potential for nuanced and context-aware analyses. Moreover, the expertise needed…

Machine Learning · Statistics 2024-12-23 James Requeima , John Bronskill , Dami Choi , Richard E. Turner , David Duvenaud

The promise of generative AI to revolutionize education is constrained by the pedagogical limits of large language models (LLMs). A major issue is the lack of access to high-quality training data that reflect the learning of actual…

Computation and Language · Computer Science 2025-10-07 Janos Perczel , Jin Chow , Dorottya Demszky

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

Due to their architecture and vast pre-training data, large language models (LLMs) demonstrate strong text classification performance. However, LLM output - here, the category assigned to a text - depends heavily on the wording of the…

Computation and Language · Computer Science 2025-12-04 Kylie L. Anglin , Stephanie Milan , Brittney Hernandez , Claudia Ventura

In the era of personalized education, the provision of comprehensible explanations for learning recommendations is of a great value to enhance the learner's understanding and engagement with the recommended learning content. Large language…

Artificial Intelligence · Computer Science 2025-01-23 Hasan Abu-Rasheed , Christian Weber , Madjid Fathi

Proteins are fundamental to biology, executing diverse functions through complex physicochemical interactions, and they hold transformative potential across medicine, materials science, and environmental applications. Protein Language…

Biomolecules · Quantitative Biology 2025-06-11 Logan Hallee , Nikolaos Rafailidis , David B. Bichara , Jason P. Gleghorn

Recent advancements highlight the success of instruction tuning with large language models (LLMs) utilizing Chain-of-Thought (CoT) data for mathematical reasoning tasks. Despite the fine-tuned LLMs, challenges persist, such as incorrect,…

Computation and Language · Computer Science 2024-03-28 Yongwei Zhou , Tiejun Zhao

Large language models (LLMs) often struggle with complex mathematical tasks, prone to "hallucinating" incorrect answers due to their reliance on statistical patterns. This limitation is further amplified in average Small LangSLMs with…

Recently, prompt tuning \cite{lester2021power} has gradually become a new paradigm for NLP, which only depends on the representation of the words by freezing the parameters of pre-trained language models (PLMs) to obtain remarkable…

Computation and Language · Computer Science 2022-01-31 Pan He , Yuxi Chen , Yan Wang , Yanru Zhang

Large Language Models (LLMs) have demonstrated remarkable capabilities in many real-world applications. Nonetheless, LLMs are often criticized for their tendency to produce hallucinations, wherein the models fabricate incorrect statements…

Computation and Language · Computer Science 2024-06-05 Qinggang Zhang , Junnan Dong , Hao Chen , Daochen Zha , Zailiang Yu , Xiao Huang

A central goal of cognitive modeling is to develop models that not only predict human behavior but also provide insight into the underlying cognitive mechanisms. While neural network models trained on large-scale behavioral data often…

Artificial Intelligence · Computer Science 2026-02-03 Jian-Qiao Zhu , Hanbo Xie , Dilip Arumugam , Robert C. Wilson , Thomas L. Griffiths

Training large language models (LLMs) with open-domain instruction following data brings colossal success. However, manually creating such instruction data is very time-consuming and labor-intensive. Moreover, humans may struggle to produce…

Computation and Language · Computer Science 2025-05-28 Can Xu , Qingfeng Sun , Kai Zheng , Xiubo Geng , Pu Zhao , Jiazhan Feng , Chongyang Tao , Qingwei Lin , Daxin Jiang

Autoregressive large language models (LLMs) pre-trained by next token prediction are inherently proficient in generative tasks. However, their performance on knowledge-driven tasks such as factual knowledge querying remains unsatisfactory.…

Computation and Language · Computer Science 2026-01-14 Peng Yu , Cheng Deng , Beiya Dai , Xinbing Wang , Ying Wen