标注词汇 (可能是) 所有你需要的
Logan Hallee1, Niko Rafailidis1, Colin Horger2
1Center for Bioinformatics and Computational Biology, University of Delaware.
bioRxiv : the preprint server for biology
|August 12, 2024
概括
我们介绍了注释词汇,一种用于蛋白质特性的新语言,使蛋白质能够有效地表示和生成模型. 这种方法增强了蛋白质注释和设计的变压器模型.
科学领域:
- 计算生物学是一种计算生物学.
- 生物信息学是一种生物信息学.
- 机器学习 机器学习
背景情况:
- 蛋白质语言模型 (pLMs) 对于计算蛋白质分析至关重要,但它们的嵌入通常集中在结构特征上.
- 需要将更广泛的生物化学特性纳入蛋白质表示中.
研究的目的:
- 开发一种创新的方法来创建蛋白质嵌入,捕获各种生物化学性质.
- 通过使用"注释词汇"来训练变压器模型,以增强蛋白质表示和生成.
- 在下游任务中证明这种新方法的效率和有效性.
主要方法:
- 设计了"注释词汇",一种基于结构化本体学的蛋白质特性转换器可读的语言.
- 训练有素的"注释转换器" (AT) 仅从描述中预测掩盖蛋白质的特性,而不依赖于氨基酸序列.
- 开发了一种新的损失函数,并利用高效的计算来训练表示模型.
- 提出了一个新的基于序列对齐的评分来评估新生成的蛋白质序列.
- 在各种模型架构中利用AT表示来进行蛋白质表示和生成.
主要成果:
- 首屈一指的表示模型CAMP在15个数据集中的5个中实现了最先进的嵌入,在其他数据集中具有竞争性性能,证明了计算效率.
- 生成模型,GSM,从仅注释提示生成了高对齐分数,许多生成的序列显示了显著的BLAST匹配和匹配注释属性.
- 词汇集成增强了变压器模型,提供了基于蛋白质描述的新数值特征空间.
结论:
- "注释词汇"提供了一种强大而有效的方法,可以通过变压器模型来增强蛋白质表示和生成.
- 这种方法提供了一个有前途的途径,可以用专业领域应用程序的本体学和知识图来取代传统的代币.
- 标注词汇促进了简洁,准确和高效的蛋白质描述,使蛋白质标注和设计的新方法成为可能.
更多相关视频
07:26Executing Complexity-Increasing Queries in Relational MySQL and NoSQL MongoDB and EXist Size-Growing ISO/EN 13606 Standardized EHR Databases
Published on: March 19, 2018
9.3K
10:23Author Spotlight: Three-Dimensional Cephalometric Landmark Annotation Demonstration on Human Cone Beam Computed Tomography Scans
Published on: September 8, 2023
2.7K
相关概念视频
01:42Schemas
11.6K
A schema is a mental construct consisting of a cluster or collection of related concepts (Bartlett, 1932). There are many different types of schemata, and they all have one thing in common: schemata are a method of organizing information that allows the brain to work more efficiently. When a schema is activated, the brain makes immediate assumptions about the person or object being observed.
11.6K
01:17Schemata
72
A schema is a mental construct that organizes related concepts, allowing the brain to process information efficiently. Upon activation, schemata facilitate assumptions about people or objects.
Two types of schemata are:
Two types of schemata are:
72
01:10Nomenclature of Aryl and Heterocyclic Amines
2.3K
The simplest aromatic amine is phenylamine, which contains an –NH2 functionality directly attached to an aromatic ring. The name aniline is designated for this skeleton. As shown in Figure 1, the common names of the functionalized anilines involve prefixes ortho-, meta-, and para- to indicate the substitution position. Different functionalized aniline derivatives also have notable trivial names.
2.3K
02:16Self-Schemas
31.1K
In general, a schema is a mental construct consisting of a cluster or collection of related concepts (Bartlett, 1932). There are many different types of schemata, and they all have one thing in common: schemata are a method of organizing information that allows the brain to work more efficiently. When a schema is activated, the brain makes immediate assumptions about the person or object being observed.
31.1K
01:29Aggregates Classification
310
Aggregate classification is generally based on its size, petrographic characteristics, weight, and source. Size classification ranges from coarse to fine aggregates, defined by the size of the particles. Coarse aggregates are particles that do not pass through ASTM sieve No. 4, and aggregates that pass through the sieve are fine aggregates.
Petrographic classification groups aggregates based on common mineralogical characteristics. Some of the common mineral groups found in aggregates are...
Petrographic classification groups aggregates based on common mineralogical characteristics. Some of the common mineral groups found in aggregates are...
310
01:11Nomenclature of Aromatic Compounds with Multiple Substituents
7.7K
When more than one substituent is present on the benzene ring, the IUPAC nomenclature depends on the number of substituents present.
For disubstituted benzene derivatives, with two groups attached to the benzene ring, three constitutional isomers are possible. For example, consider dimethyl benzene, often called xylene, where the second methyl group can be substituted at the second, third, or fourth carbon. The relative position of the substituents is represented by prefixes ortho, meta, or...
For disubstituted benzene derivatives, with two groups attached to the benzene ring, three constitutional isomers are possible. For example, consider dimethyl benzene, often called xylene, where the second methyl group can be substituted at the second, third, or fourth carbon. The relative position of the substituents is represented by prefixes ortho, meta, or...
7.7K