AIPs-SnTCN:使用快速文本和转换器编码器基于混合词嵌入与自我规范化的时间卷积网络预测抗炎
Ali Raza1,2, Jamal Uddin1, Abdullah Almuhaimeed3
1Department of Physical and Numerical Sciences, Qurtuba University of Science and Information Technology, Peshawar, Khyber Pakhtunkhwa 25124, Pakistan.
Journal of chemical information and modeling
|October 31, 2023
概括
我们开发了AIPs-SnTCN,这是一个新的计算模型,可以准确预测抗炎. 这种方法为慢性炎症疾病的传统治疗提供了具有成本效益和效率的替代方案.
科学领域:
- 生物化学 生物化学
- 计算生物学 计算生物学
- 药理学 药理学是指药理学的学科.
背景情况:
- 炎症是对受伤或感染的关键生物反应,但长时间的炎症会导致慢性疾病.
- 目前用于湿实验室治疗炎症的方法昂贵,耗时,并且可能损害健康细胞.
- 类治疗药物在向患病细胞方面具有很高的特异性,是有前途的替代品.
研究的目的:
- 开发一种高精度的计算模型,用于预测抗炎.
- 为了利用先进的机器学习技术用于基于的药物发现.
- 为识别潜在的抗炎药物提供一种更有效和更具成本效益的方法.
主要方法:
- 用词嵌入 (skip-gram,BERT) 和联合三元特征 (CTF) 来编码样.
- 一个融合向量结合了词嵌入和顺序特征,以克服个人限制.
- 支持矢量机器-递归特征消除 (SVM-RFE) 优化的特征选择.
- 改进的自我规范化的时卷积网络 (SnTCN) 用于模型训练.
主要成果:
- AIPs-SnTCN模型在培训数据上实现了95.86%的准确性和0.97 AUC.
- 在一个独立的数据集上,该模型获得了92.04%的准确性和0.96 AUC.
- AIPs-SnTCN显著优于现有模型,显示~19%更高的精度和~14%更高的AUC.
结论:
- AIPs-SnTCN是一种可靠和有效的计算工具,用于预测抗炎.
- 该模型显示了加速制药设计和学术研究的巨大潜力.
- 这种方法在针对炎症状况的向类疗法的开发中提供了宝贵的进步.
相关概念视频
Transformers
1.1K
A device that transforms voltages from one value to another using induction is called a transformer. A transformer consists of two separate coils, or windings, wrapped around the same soft iron core. However, they are electrically insulated from each other.
The iron core has a substantial relative permeability. Therefore, the magnetic field lines generated due to the current in one winding are almost entirely confined within the core, such that the same magnetic flux permeates each turn of both...
The iron core has a substantial relative permeability. Therefore, the magnetic field lines generated due to the current in one winding are almost entirely confined within the core, such that the same magnetic flux permeates each turn of both...
1.1K
Prediction Intervals
2.3K
The interval estimate of any variable is known as the prediction interval. It helps decide if a point estimate is dependable.
However, the point estimate is most likely not the exact value of the population parameter, but close to it. After calculating point estimates, we construct interval estimates, called confidence intervals or prediction intervals. This prediction interval comprises a range of values unlike the point estimate and is a better predictor of the observed sample value, y.
However, the point estimate is most likely not the exact value of the population parameter, but close to it. After calculating point estimates, we construct interval estimates, called confidence intervals or prediction intervals. This prediction interval comprises a range of values unlike the point estimate and is a better predictor of the observed sample value, y.
2.3K
Peptide Identification Using Tandem Mass Spectrometry
6.5K
Tandem mass spectrometry, also known as MS/MS or MS2, is an analytical technique that employs two mass analyzers. Essentially it is a series of mass spectrometers that helps isolate a particular biomolecule and then helps study its chemical properties.
This technique helps gather information regarding the protein from which the peptide was obtained and to study the peptides’ amino acid sequence. Identifying peptides from a complex mixture is an important component of the growing field of...
This technique helps gather information regarding the protein from which the peptide was obtained and to study the peptides’ amino acid sequence. Identifying peptides from a complex mixture is an important component of the growing field of...
6.5K
Improving Translational Accuracy
11.4K
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...
11.4K
Fast Fourier Transform
349
The Fast Fourier Transform (FFT) is a computational algorithm designed to compute the Discrete Fourier Transform (DFT) efficiently. By breaking down the calculations into smaller, manageable sections, the FFT significantly reduces the computational complexity involved. Direct computation of an N-point DFT requires N2 complex multiplications, whereas the FFT algorithm needs only (N/2)log2N multiplications, offering a much faster performance.
The computational efficiency of the FFT becomes...
The computational efficiency of the FFT becomes...
349
End Point Prediction: Gran Plot
345
A Gran plot is used to predict the equivalence volume or endpoint of a potentiometric or acid-base titration without reaching the endpoint. Typically, titration data is collected as a function of the titrant's volume up to a point less than the equivalence volume and then transformed into a linear format. The straight line is extended to the x-axis, indicating the necessary titrant volume to achieve the equivalence point.
For potentiometric titration, the Gran plot is created by plotting...
For potentiometric titration, the Gran plot is created by plotting...
345


