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There is increasing adoption of artificial intelligence in drug discovery. However, existing studies use machine learning to mainly utilize the chemical structures of molecules but ignore the vast textual knowledge available in chemistry.…

Machine Learning · Computer Science 2024-01-31 Shengchao Liu , Weili Nie , Chengpeng Wang , Jiarui Lu , Zhuoran Qiao , Ling Liu , Jian Tang , Chaowei Xiao , Anima Anandkumar

The versatility of multimodal deep learning holds tremendous promise for advancing scientific research and practical applications. As this field continues to evolve, the collective power of cross-modal analysis promises to drive…

Machine Learning · Computer Science 2025-05-15 Yifei Wang , Yunrui Li , Lin Liu , Pengyu Hong , Hao Xu

Despite the wealth of single-cell multi-omics data, it remains challenging to predict the consequences of novel genetic and chemical perturbations in the human body. It requires knowledge of molecular interactions at all biological levels,…

Artificial Intelligence · Computer Science 2025-01-22 You Wu , Lei Xie

Machine learning models of vastly different modalities and architectures are being trained to predict the behavior of molecules, materials, and proteins. However, it remains unclear whether they learn similar internal representations of…

Machine Learning · Computer Science 2025-12-04 Sathya Edamadaka , Soojung Yang , Ju Li , Rafael Gómez-Bombarelli

The prediction of molecular properties is a crucial task in the field of material and drug discovery. The potential benefits of using deep learning techniques are reflected in the wealth of recent literature. Still, these techniques are…

Machine Learning · Computer Science 2023-09-06 Minghao Guo , Veronika Thost , Samuel W Song , Adithya Balachandran , Payel Das , Jie Chen , Wojciech Matusik

AI models are increasingly required to be multimodal, integrating disparate input streams into a coherent state representation on which subsequent behaviors and actions can be based. This paper seeks to understand how such models behave…

Computation and Language · Computer Science 2025-07-03 Tianze Hua , Tian Yun , Ellie Pavlick

Natural language is expected to be a key medium for various human-machine interactions in the era of large language models. When it comes to the biochemistry field, a series of tasks around molecules (e.g., property prediction, molecule…

Computation and Language · Computer Science 2023-06-22 Zheni Zeng , Bangchen Yin , Shipeng Wang , Jiarui Liu , Cheng Yang , Haishen Yao , Xingzhi Sun , Maosong Sun , Guotong Xie , Zhiyuan Liu

The field of chemistry and Artificial Intelligence (AI) intersection is an area of active research that aims to accelerate scientific discovery. The integration of large language models (LLMs) with scientific modalities has shown…

Computation and Language · Computer Science 2024-07-16 Dimitris Gkoumas

Molecular property prediction is essential for applications such as drug discovery and toxicity assessment. While Graph Neural Networks (GNNs) have shown promising results by modeling molecules as molecular graphs, their reliance on…

Machine Learning · Computer Science 2025-04-09 Tianyi Jiang , Zeyu Wang , Shanqing Yu , Qi Xuan

The ability to reason with and integrate different sensory inputs is the foundation underpinning human intelligence and it is the reason for the growing interest in modelling multi-modal information within Knowledge Graphs. Multi-Modal…

Artificial Intelligence · Computer Science 2024-10-18 Gianluca Apriceno , Valentina Tamma , Tania Bailoni , Jacopo de Berardinis , Mauro Dragoni

The emoticons are symbolic representations that generally accompany the textual content to visually enhance or summarize the true intention of a written message. Although widely utilized in the realm of social media, the core semantics of…

Computer Vision and Pattern Recognition · Computer Science 2024-08-06 Ananya Pandey , Dinesh Kumar Vishwakarma

In real-world scenarios, many data processing problems often involve heterogeneous images associated with different imaging modalities. Since these multimodal images originate from the same phenomenon, it is realistic to assume that they…

Computer Vision and Pattern Recognition · Computer Science 2021-03-11 Pingfan Song , Miguel R. D. Rodrigues

Grounded language models use external sources of information, such as knowledge graphs, to meet some of the general challenges associated with pre-training. By extending previous work on compositional generalization in semantic parsing, we…

Computation and Language · Computer Science 2024-06-10 Sondre Wold , Étienne Simon , Lucas Georges Gabriel Charpentier , Egor V. Kostylev , Erik Velldal , Lilja Øvrelid

Designing molecules with specific properties is a long-lasting research problem and is central to advancing crucial domains such as drug discovery and material science. Recent advances in deep graph generative models treat molecule design…

Machine Learning · Computer Science 2022-03-02 Yuanqi Du , Xiaojie Guo , Amarda Shehu , Liang Zhao

Unlike vision and language data which usually has a unique format, molecules can naturally be characterized using different chemical formulations. One can view a molecule as a 2D graph or define it as a collection of atoms located in a 3D…

Machine Learning · Computer Science 2023-03-29 Shengjie Luo , Tianlang Chen , Yixian Xu , Shuxin Zheng , Tie-Yan Liu , Liwei Wang , Di He

Recent advancements in artificial intelligence have sparked interest in scientific assistants that could support researchers across the full spectrum of scientific workflows, from literature review to experimental design and data analysis.…

Artificial intelligence (AI) is increasingly used for the inverse design of materials, such as crystals and molecules. Existing AI research on molecules has integrated chemical structures of molecules with textual knowledge to adapt to…

Computation and Language · Computer Science 2025-02-25 Yang Jeong Park , Mayank Kumaran , Chia-Wei Hsu , Elsa Olivetti , Ju Li

In recent years, AI models that mine intrinsic patterns from molecular structures and protein sequences have shown promise in accelerating drug discovery. However, these methods partly lag behind real-world pharmaceutical approaches of…

Machine Learning · Computer Science 2023-10-17 Yizhen Luo , Xing Yi Liu , Kai Yang , Kui Huang , Massimo Hong , Jiahuan Zhang , Yushuai Wu , Zaiqing Nie

We consider feature representation learning problem of molecular graphs. Graph Neural Networks have been widely used in feature representation learning of molecular graphs. However, most existing methods deal with molecular graphs…

Machine Learning · Computer Science 2022-06-08 Zhaoning Yu , Hongyang Gao
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