对分子表示学习基础模型的系统审查
Bosheng Song1, Jiayi Zhang1, Ying Liu1
1College of Computer Science and Electronic Engineering, Hunan University, 116 Lushan South Road, Yuelu District, 410086 Changsha, China.
Briefings in bioinformatics
|January 9, 2026
概括
分子表示学习 (MRL) 使用基础模型将分子数据转换为药物发现的数值向量. 这些先进的模型增强了数据的概括性和适应性,推动了计算化学的创新.
科学领域:
- 计算化学的计算化学
- 机器学习 机器学习
- 药物发现 药物发现 药物发现
背景情况:
- 分子表示学习 (MRL) 将分子结构转化为数值向量,用于计算分析.
- 基础模型为MRL提供了新的机会,提高了普遍性和性能,特别是在有限的数据的情况下.
研究的目的:
- 在MRL中审查当前的分子描述符,数据集和基础模型.
- 将基础模型分类并分析MRL的预训练策略.
- 讨论MRL基础模型在药物发现中的应用和解释性.
主要方法:
- 基础模型的分类为基于单模和基于多模的类别.
- 评价代表性模型,它们的优点和缺点.
- 对MRL基础模型的四个核心预培训策略的系统摘要.
主要成果:
- 基础模型通过预训练和微调来提高概括性和适应性来提高MRL.
- 确定并评估了MRL的单模和多模基础模型.
- 分析了预训练策略及其对药物发现下游任务的影响.
结论:
- 在推进计算药物发现方面,MRL基础模型至关重要.
- 未来的方向包括提高模型的解释性和探索新的预训练技术.
- 该审查提供了对小分子的MRL基础模型的全面概述.
相关概念视频
Molecular Models
43.5K
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.
43.5K
Mechanistic Models: Compartment Models in Algorithms for Numerical Problem Solving
282
Mechanistic models play a crucial role in algorithms for numerical problem-solving, particularly in nonlinear mixed effects modeling (NMEM). These models aim to minimize specific objective functions by evaluating various parameter estimates, leading to the development of systematic algorithms. In some cases, linearization techniques approximate the model using linear equations.
In individual population analyses, different algorithms are employed, such as Cauchy's method, which uses a...
In individual population analyses, different algorithms are employed, such as Cauchy's method, which uses a...
282
Classification of Systems-I
544
Linearity is a system property characterized by a direct input-output relationship, combining homogeneity and additivity.
Homogeneity dictates that if an input x(t) is multiplied by a constant c, the output y(t) is multiplied by the same constant. Mathematically, this is expressed as:
Homogeneity dictates that if an input x(t) is multiplied by a constant c, the output y(t) is multiplied by the same constant. Mathematically, this is expressed as:
544
Predicting Molecular Geometry
44.7K
VSEPR Theory for Determination of Electron Pair Geometries
44.7K
Molecular Shapes
61.2K
Molecules have characteristic shapes that are crucial for their function. The arrangement of various electron groups around the central atom dictates their molecular geometry. Electron pairs in the valence shell of a central atom will adopt an arrangement that minimizes repulsions between the electron pairs by maximizing the distance between them. The valence electrons form either bonding pairs, located primarily between bonded atoms, or lone pairs.
Two regions of electron density in a diatomic...
Two regions of electron density in a diatomic...
61.2K
Classification of Systems-II
453
Continuous-time systems have continuous input and output signals, with time measured continuously. These systems are generally defined by differential or algebraic equations. For instance, in an RC circuit, the relationship between input and output voltage is expressed through a differential equation derived from Ohm's law and the capacitor relation,
453


