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This paper introduces diffusion protein language model (DPLM), a versatile protein language model that demonstrates strong generative and predictive capabilities for protein sequences. We first pre-train scalable DPLMs from…

Machine Learning · Computer Science 2024-10-17 Xinyou Wang , Zaixiang Zheng , Fei Ye , Dongyu Xue , Shujian Huang , Quanquan Gu

Parameter generation has emerged as a novel paradigm for neural network development, offering an alternative to traditional neural network training by synthesizing high-quality model weights directly. In the context of Low-Rank Adaptation…

Machine Learning · Computer Science 2025-04-10 Rana Muhammad Shahroz Khan , Dongwen Tang , Pingzhi Li , Kai Wang , Tianlong Chen

Generative models in molecular design tend to be richly parameterized, data-hungry neural models, as they must create complex structured objects as outputs. Estimating such models from data may be challenging due to the lack of sufficient…

Machine Learning · Computer Science 2021-08-17 Kevin Yang , Wengong Jin , Kyle Swanson , Regina Barzilay , Tommi Jaakkola

Pre-trained large language models (PLMs) underlie most new developments in natural language processing. They have shifted the field from application-specific model pipelines to a single model that is adapted to a wide range of tasks.…

Computation and Language · Computer Science 2023-06-30 Joshua Maynez , Priyanka Agrawal , Sebastian Gehrmann

Designing functional transition metal complexes (TMCs) faces challenges due to the vast search space of metals and ligands, requiring efficient optimization strategies. Traditional genetic algorithms (GAs) are commonly used, employing…

Chemical Physics · Physics 2024-10-25 Jieyu Lu , Zhangde Song , Qiyuan Zhao , Yuanqi Du , Yirui Cao , Haojun Jia , Chenru Duan

Discovery of novel and promising materials is a critical challenge in the field of chemistry and material science, traditionally approached through methodologies ranging from trial-and-error to machine learning-driven inverse design. Recent…

Machine Learning · Computer Science 2024-12-13 Dong Hyeon Mok , Seoin Back

We analyze the capabilities of Transformer language models in learning compositional discrete tasks. To this end, we evaluate training LLaMA models and prompting GPT-4 and Gemini on four tasks demanding to learn a composition of several…

Conditional layout generation aims to automatically generate visually appealing and semantically coherent layouts from user-defined constraints. While recent methods based on generative models have shown promising results, they typically…

Computer Vision and Pattern Recognition · Computer Science 2026-02-06 Hengyu Shi , Junhao Su , Tianyang Han , Junfeng Luo , Jialin Gao

In the domain of model-based engineering, models are essential components that enable system design and analysis. Traditionally, the creation of these models has been a manual process requiring not only deep modeling expertise but also…

Software Engineering · Computer Science 2025-03-31 Fengjunjie Pan , Nenad Petrovic , Vahid Zolfaghari , Long Wen , Alois Knoll

Molecule design is a multifaceted approach that leverages computational methods and experiments to optimize molecular properties, fast-tracking new drug discoveries, innovative material development, and more efficient chemical processes.…

Computation and Language · Computer Science 2024-08-23 Sakhinana Sagar Srinivas , Venkataramana Runkana

Despite a widespread success in various applications, large language models (LLMs) often stumble when tackling basic physical reasoning or executing robotics tasks, due to a lack of direct experience with the physical nuances of the real…

Computation and Language · Computer Science 2024-11-13 Haolan Liu , Jishen Zhao

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

Modern generative pre-trained language models excel at open-ended text generation, yet continue to underperform on structure-related tasks such as NER, relation extraction, and semantic role labeling, especially when compared to…

Computation and Language · Computer Science 2025-12-23 Minho Lee , Junghyun Min , Yerang Kim , Woochul Lee , Yeonsoo Lee

This work presents AdditiveLLM2 a multi-modal, domain adapted large language model built upon the instruction tuned variant of the Gemma 3 model using a relatively small dataset of around 50 million tokens. The dataset (AdditiveLLM2-OA)…

Machine Learning · Computer Science 2026-03-24 Peter Pak , Amir Barati Farimani

ProMoAI is a novel tool that leverages Large Language Models (LLMs) to automatically generate process models from textual descriptions, incorporating advanced prompt engineering, error handling, and code generation techniques. Beyond…

Databases · Computer Science 2024-08-09 Humam Kourani , Alessandro Berti , Daniel Schuster , Wil M. P. van der Aalst

In the molecular domain, numerous studies have explored the use of multimodal large language models (LLMs) to construct a general-purpose, multi-task molecular model. However, these efforts are still far from achieving a truly universal…

Machine Learning · Computer Science 2025-10-31 Chengxin Hu , Hao Li , Yihe Yuan , Zezheng Song , Chenyang Zhao , Haixin Wang

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

This work introduces a method to tune a sequence-based generative model for molecular de novo design that through augmented episodic likelihood can learn to generate structures with certain specified desirable properties. We demonstrate how…

Artificial Intelligence · Computer Science 2017-08-30 Marcus Olivecrona , Thomas Blaschke , Ola Engkvist , Hongming Chen

Scaling language models with more data, compute and parameters has driven significant progress in natural language processing. For example, thanks to scaling, GPT-3 was able to achieve strong results on in-context learning tasks. However,…

Automatic layout generation that can synthesize high-quality layouts is an important tool for graphic design in many applications. Though existing methods based on generative models such as Generative Adversarial Networks (GANs) and…

Computer Vision and Pattern Recognition · Computer Science 2023-05-05 Shang Chai , Liansheng Zhuang , Fengying Yan