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Deep generative models of molecules have grown immensely in popularity, trained on relevant datasets, these models are used to search through chemical space. The downstream utility of generative models for the inverse design of novel…

Machine Learning · Computer Science 2023-05-11 Daniel Flam-Shepherd , Kevin Zhu , Alán Aspuru-Guzik

Molecular generative models, often employing GPT-style language modeling on molecular string representations, have shown promising capabilities when scaled to large datasets and model sizes. However, it remains unclear and subject to debate…

Machine Learning · Computer Science 2026-02-02 Dong Xu , Qihua Pan , Sisi Yuan , Jianqiang Li , Zexuan Zhu , Junkai Ji

The generation of molecules with desired properties has become increasingly popular, revolutionizing the way scientists design molecular structures and providing valuable support for chemical and drug design. However, despite the potential…

Machine Learning · Computer Science 2024-03-05 Yin Fang , Ningyu Zhang , Zhuo Chen , Lingbing Guo , Xiaohui Fan , Huajun Chen

Advancements in natural language generation (NLG) and large language models (LLMs) have led to proficient text generation in various tasks. However, integrating intricate constraints into neural text generation, due to LLMs' opacity,…

Computation and Language · Computer Science 2024-03-22 Xiang Chen , Xiaojun Wan

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

This paper addresses the challenges of high computational cost and slow inference in deploying large language models. It proposes a distillation strategy guided by multiple teacher models. The method constructs several teacher models and…

Computation and Language · Computer Science 2025-07-22 Xiandong Meng , Yan Wu , Yexin Tian , Xin Hu , Tianze Kang , Junliang Du

Large Language Models (LLMs) have revolutionised the field of Natural Language Processing (NLP) and have achieved state-of-the-art performance in practically every task in this field. However, the prevalent approach used in text generation,…

Computation and Language · Computer Science 2024-08-12 Nicolo Micheletti , Samuel Belkadi , Lifeng Han , Goran Nenadic

Large Language Models (LLMs) have demonstrated a powerful ability for text generation. However, achieving optimal results with a given prompt or instruction can be challenging, especially for billion-sized models. Additionally, undesired…

Computation and Language · Computer Science 2024-10-07 Lifu Tu , Semih Yavuz , Jin Qu , Jiacheng Xu , Rui Meng , Caiming Xiong , Yingbo Zhou

Recent advancements in large language models have opened new possibilities for generative molecular drug design. We present Chemlactica and Chemma, two language models fine-tuned on a novel corpus of 110M molecules with computed properties,…

Self-supervised neural language models have recently found wide applications in generative design of organic molecules and protein sequences as well as representation learning for downstream structure classification and functional…

Materials Science · Physics 2022-09-21 Lai Wei , Nihang Fu , Yuqi Song , Qian Wang , Jianjun Hu

The remarkable success of Large Language Models (LLMs) across diverse tasks has driven the research community to extend their capabilities to molecular applications. However, most molecular LLMs employ adapter-based architectures that do…

Computation and Language · Computer Science 2025-06-24 Shuhan Guo , Yatao Bian , Ruibing Wang , Nan Yin , Zhen Wang , Quanming Yao

Self-supervised neural language models have recently achieved unprecedented success, from natural language processing to learning the languages of biological sequences and organic molecules. These models have demonstrated superior…

Natural products are substances produced by organisms in nature and often possess biological activity and structural diversity. Drug development based on natural products has been common for many years. However, the intricate structures of…

Biomolecules · Quantitative Biology 2024-11-21 Koh Sakano , Kairi Furui , Masahito Ohue

The rapid advancement of large language models (LLMs) such as GPT-3, PaLM, and Llama has significantly transformed natural language processing, showcasing remarkable capabilities in understanding and generating language. However, a…

Computation and Language · Computer Science 2026-05-15 Yifan Zhang

Molecular generation and molecular property prediction are both crucial for drug discovery, but they are often developed independently. Inspired by recent studies, which demonstrate that diffusion model, a prominent generative approach, can…

Machine Learning · Computer Science 2025-04-07 Shikun Feng , Yuyan Ni , Yan Lu , Zhi-Ming Ma , Wei-Ying Ma , Yanyan Lan

Knowledge distillation plays a key role in compressing the Large Language Models (LLMs), which boosts a small-size student model under large teacher models' guidance. However, existing LLM distillation methods overly rely on…

Computation and Language · Computer Science 2024-07-16 Xiaoyu Liu , Yun Zhang , Wei Li , Simiao Li , Xudong Huang , Hanting Chen , Yehui Tang , Jie Hu , Zhiwei Xiong , Yunhe Wang

Generating novel molecules is challenging, with most representations leading to generative models producing many invalid molecules. Spanning Tree-based Graph Generation (STGG) is a promising approach to ensure the generation of valid…

Machine Learning · Computer Science 2025-07-17 Alexia Jolicoeur-Martineau , Aristide Baratin , Kisoo Kwon , Boris Knyazev , Yan Zhang

Proteins adopt multiple structural conformations to perform their diverse biological functions, and understanding these conformations is crucial for advancing drug discovery. Traditional physics-based simulation methods often struggle with…

Biomolecules · Quantitative Biology 2025-03-14 Jiarui Lu , Xiaoyin Chen , Stephen Zhewen Lu , Chence Shi , Hongyu Guo , Yoshua Bengio , Jian Tang

Molecular generation plays an important role in drug discovery and materials science, especially in data-scarce scenarios where traditional generative models often struggle to achieve satisfactory conditional generalization. To address this…

Machine Learning · Computer Science 2025-05-13 Zimo Yan , Jie Zhang , Zheng Xie , Chang Liu , Yizhen Liu , Yiping Song

Virtual Labs offer valuable opportunities for hands-on, inquiry-based science learning, yet teachers often struggle to adapt them to fit their instructional goals. Third-party materials may not align with classroom needs, and developing…

Computation and Language · Computer Science 2025-10-09 R. Alexander Knipper , Indrani Dey , Souvika Sarkar , Hari Narayanan , Sadhana Puntambekar , Santu Karmaker