通过知识提示来改善多模式分子预训练
Yang Li1, Chang Liu1, Xin Gao2,3,4
1College of Computer and Control Engineering, Northeast Forestry University, Harbin, 150040, China.
Bioinformatics (Oxford, England)
|August 23, 2025
概括
一个新的框架MolPrompt通过整合分子图表和文本来增强分子预训练. 这种知识增强的方法改善了药物发现任务,如属性预测和抑制剂识别.
科学领域:
- 计算药物发现
- 化学信息学
- 用于化学的机器学习
背景情况:
- 分子预训是计算药物发现的关键,
- 现有的方法往往忽略了物理化学性质,重点是结构.
- 整合不同的分子数据对于先进的药物发现至关重要.
研究的目的:
- 推出一个新的知识增强多式预培训框架MolPrompt.
- 整合分子图表和文本描述以改善分子表示.
- 通过纳入领域知识来增强结构意识的表现学习.
主要方法:
- 使用Graphormer和BERT的双编码架构.
- 使用对比学习来整合分子图形和文本.
- 将知识提示 (来自分子描述器的语义嵌入) 引入图形编码器.
主要成果:
- 在多个任务中表现出卓越的表现.
- 在分子性质预测和毒性估计方面取得了最先进的结果.
- 展示了改善的跨模式检索和抗癌抑制剂识别.
结论:
- 增强知识的多式预训练显著改善了分子表示.
- 将领域知识整合到结构学习中可以提高深度和可解释性.
- MolPrompt为计算药物发现应用提供了更有效的方法.
相关概念视频
Molecular Models
40.4K
Physical models representing molecular architectures of chemical compounds play essential roles in understanding chemistry. The use of molecular models makes it easier to visualize the structures and shapes of atoms and molecules.
40.4K
Improving Translational Accuracy
11.9K
Base complementarity between the three base pairs of mRNA codon and the tRNA anticodon is not a failsafe mechanism. Inaccuracies can range from a single mismatch to no correct base pairing at all. The free energy difference between the correct and nearly correct base pairs can be as small as 3 kcal/ mol. With complementarity being the only proofreading step, the estimated error frequency would be one wrong amino acid in every 100 amino acids incorporated. However, error frequencies observed in...
11.9K
Multi-input and Multi-variable systems
149
Cruise control systems in cars are designed as multi-input systems to maintain a driver's desired speed while compensating for external disturbances such as changes in terrain. The block diagram for a cruise control system typically includes two main inputs: the desired speed set by the driver and any external disturbances, such as the incline of the road. By adjusting the engine throttle, the system maintains the vehicle's speed as close to the desired value as possible.
In the absence...
In the absence...
149
Predicting Molecular Geometry
35.9K
VSEPR Theory for Determination of Electron Pair Geometries
35.9K
Multi-species Conserved Sequences
4.3K
Next-generation sequencing technologies have created large genomic databases of a variety of animals and plants. Ever since the human genome project was completed, scientists studied the genome of primates, mammals, and other phylogenetically distant living beings. Such large-scale studies have provided new insights into the evolutionary relationship between organisms.
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved...
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved...
4.3K
Molecular Kinetic Energy
5.2K
The word "gas" comes from the Flemish word meaning "chaos," first used to describe vapors by the chemist J. B. van Helmont. Consider a container filled with gas, with a continuous and random motion of molecules. During collisions, the velocity component parallel to the wall is unchanged, and the component perpendicular to the wall reverses direction but does not change in magnitude. If the molecule’s velocity changes in the x-direction, then its momentum is changed.
5.2K


