English
Related papers

Related papers: Controllable Protein Sequence Generation with LLM …

200 papers

Recent developments in pretrained large language models (LLMs) applied to robotics have demonstrated their capacity for sequencing a set of discrete skills to achieve open-ended goals in simple robotic tasks. In this paper, we examine the…

Robotics · Computer Science 2024-09-09 Aidan Curtis , Nishanth Kumar , Jing Cao , Tomás Lozano-Pérez , Leslie Pack Kaelbling

Designing therapeutic peptides with tailored properties is hindered by the vastness of sequence space, limited experimental data, and poor interpretability of current generative models. To address these challenges, we introduce PepThink-R1,…

Machine Learning · Computer Science 2026-03-30 Ruheng Wang , Hang Zhang , Trieu Nguyen , Shasha Feng , Hao-Wei Pang , Xiang Yu , Li Xiao , Peter Zhiping Zhang

Length control in Large Language Models (LLMs) is a crucial but under-addressed challenge, with applications ranging from voice interfaces requiring concise responses to research summaries needing comprehensive outputs. Current approaches…

Computation and Language · Computer Science 2025-11-04 Adewale Akinfaderin , Shreyas Subramanian , Akarsha Sehwag

LLMs have demonstrated commendable performance across diverse domains. Nevertheless, formulating high-quality prompts to assist them in their work poses a challenge for non-AI experts. Existing research in prompt engineering suggests…

Computation and Language · Computer Science 2024-09-23 Ming Wang , Yuanzhong Liu , Xiaoyu Liang , Yijie Huang , Daling Wang , Xiaocui Yang , Sijia Shen , Shi Feng , Xiaoming Zhang , Chaofeng Guan , Yifei Zhang

The manufacturing industry is undergoing a transformative shift, driven by cutting-edge technologies like 5G, AI, and cloud computing. Despite these advancements, effective system control, which is crucial for optimizing production…

Robotics · Computer Science 2025-03-07 Muhammad Waseem , Kshitij Bhatta , Chen Li , Qing Chang

The conditional generation of proteins with desired functions is a key goal for generative models. Existing methods based on prompting of protein language models (PLMs) can generate proteins conditioned on a target functionality, such as a…

Biomolecules · Quantitative Biology 2025-06-13 Jason Yang , Aadyot Bhatnagar , Jeffrey A. Ruffolo , Ali Madani

Large Language Models (LLMs) have made great strides in areas such as language processing and computer vision. Despite the emergence of diverse techniques to improve few-shot learning capacity, current LLMs fall short in handling the…

Biomolecules · Quantitative Biology 2024-05-14 Xianggen Liu , Yan Guo , Haoran Li , Jin Liu , Shudong Huang , Bowen Ke , Jiancheng Lv

Large language model (LLM) routing has emerged as a crucial strategy for balancing computational costs with performance by dynamically assigning queries to the most appropriate model based on query complexity. Despite recent advances…

Computation and Language · Computer Science 2025-04-11 Aly M. Kassem , Bernhard Schölkopf , Zhijing Jin

Large language models (LLMs) and prompt engineering hold significant potential for advancing computer programming education through personalized instruction. This paper explores this potential by investigating three critical research…

Artificial Intelligence · Computer Science 2024-07-09 Tianyu Wang , Nianjun Zhou , Zhixiong Chen

Fine-tuned pre-trained language models (PLMs) have achieved awesome performance on almost all NLP tasks. By using additional prompts to fine-tune PLMs, we can further stimulate the rich knowledge distributed in PLMs to better serve…

Computation and Language · Computer Science 2021-09-16 Xu Han , Weilin Zhao , Ning Ding , Zhiyuan Liu , Maosong Sun

Prompt engineering is critical for the development of LLM-based applications. However, it is usually done manually in a "trial and error" fashion that can be time consuming, ineffective, and sub-optimal. Even for the prompts which seemingly…

Artificial Intelligence · Computer Science 2024-06-11 Weize Kong , Spurthi Amba Hombaiah , Mingyang Zhang , Qiaozhu Mei , Michael Bendersky

Large language models (LLMs) have revolutionized a large variety of NLP tasks. An active debate is to what extent they can do reasoning and planning. Prior work has assessed the latter in the specific context of PDDL planning, based on…

Artificial Intelligence · Computer Science 2025-05-05 Katharina Stein , Daniel Fišer , Jörg Hoffmann , Alexander Koller

This paper presents a novel approach to aligning large language models (LLMs) with individual human preferences, sometimes referred to as Reinforcement Learning from \textit{Personalized} Human Feedback (RLPHF). Given stated preferences…

Artificial Intelligence · Computer Science 2024-07-08 Jin Peng Zhou , Katie Z Luo , Jingwen Gu , Jason Yuan , Kilian Q. Weinberger , Wen Sun

This research investigates prompt designs of evaluating generated texts using large language models (LLMs). While LLMs are increasingly used for scoring various inputs, creating effective prompts for open-ended text evaluation remains…

Computation and Language · Computer Science 2024-06-28 KuanChao Chu , Yi-Pei Chen , Hideki Nakayama

Antibody therapeutics are among the most successful modern medicines, yet computationally designing antibodies with desirable binding and developability properties remains challenging. While protein language models (pLMs) have emerged as…

Machine Learning · Computer Science 2026-05-11 Justin Sanders , Luca Giancardo , Lan Guo , Yue Zhao , Kemal Sonmez , Nina Cheng , Melih Yilmaz

Protein language models (PLMs) have advanced computational protein science through large-scale pretraining and scalable architectures. In parallel, reinforcement learning (RL) has broadened exploration and enabled precise multi-objective…

The advancement of Large Language Models (LLMs), including GPT-4, provides exciting new opportunities for generative design. We investigate the application of this tool across the entire design and manufacturing workflow. Specifically, we…

We introduce RosettaSearch, an inference-time multi-objective optimization approach for backbone conditioned protein sequence design. We use large language models (LLMs) as a generative optimizer within a search algorithm capable of…

Large Language Models (LLMs) have shown promising progress for generating Register Transfer Level (RTL) hardware designs, largely because they can rapidly propose alternative architectural realizations. However, single-shot LLM generation…

Hardware Architecture · Computer Science 2026-04-20 Shiva Ahir , Prajna Bhat , Alex Doboli

Visual programming languages (VPLs) allow users to create programs through graphical interfaces, which results in easier accessibility and their widespread usage in various domains. To further enhance this accessibility, recent research has…

Computation and Language · Computer Science 2025-05-26 Deokhyung Kang , Jeonghun Cho , Yejin Jeon , Sunbin Jang , Minsub Lee , Jawoon Cho , Gary Geunbae Lee