Protein Structure Prediction and Interpretation with Support Vector Machines and Decision Trees
نویسنده
چکیده
Prediction of protein structures from protein sequences using computers is an important step to discover proteins' 3D conformation structures and their functions and hence has profound theoretical and practical significance in areas such as protein engineering and drug design. In this talk, we will discuss our new results in protein secondary structure and Transmembrane protein prediction using Support Vector Machines. We will also discuss how to use a combination of Support Vector Machine and Decision Tree to understand how a prediction is reached through rule extraction. Clearly, a good interpretation is useful for guiding biological experiments and may lead further prediction improvement. A novel approach of rule clustering for super-rule generation will also be briefly discussed.
منابع مشابه
A Comparative Study of Extreme Learning Machines and Support Vector Machines in Prediction of Sediment Transport in Open Channels
The limiting velocity in open channels to prevent long-term sedimentation is predicted in this paper using a powerful soft computing technique known as Extreme Learning Machines (ELM). The ELM is a single Layer Feed-forward Neural Network (SLFNN) with a high level of training speed. The dimensionless parameter of limiting velocity which is known as the densimetric Froude number (Fr) is predicte...
متن کاملProtein Secondary Structure Prediction: a Literature Review with Focus on Machine Learning Approaches
DNA sequence, containing all genetic traits is not a functional entity. Instead, it transfers to protein sequences by transcription and translation processes. This protein sequence takes on a 3D structure later, which is a functional unit and can manage biological interactions using the information encoded in DNA. Every life process one can figure is undertaken by proteins with specific functio...
متن کاملTransmembrane segments prediction and understanding using support vector machine and decision tree
In recent years, there have been many studies focusing on improving the accuracy of prediction of transmembrane segments, and many significant results have been achieved. In spite of these considerable results, the existing methods lack the ability to explain the process of how a learning result is reached and why a prediction decision is made. The explanation of a decision made is important fo...
متن کاملSeparating Well Log Data to Train Support Vector Machines for Lithology Prediction in a Heterogeneous Carbonate Reservoir
The prediction of lithology is necessary in all areas of petroleum engineering. This means that to design a project in any branch of petroleum engineering, the lithology must be well known. Support vector machines (SVM’s) use an analytical approach to classification based on statistical learning theory, the principles of structural risk minimization, and empirical risk minimization. In this res...
متن کاملTowards Better Understanding of Protein Secondary Structure: Extracting Prediction Rules
Although numerous computational techniques have been applied to predict protein secondary structure (PSS), only limited studies have dealt with discovery of logic rules underlying the prediction itself. Such rules offer interesting links between the prediction model and the underlying biology. In addition, they enhance interpretability of PSS prediction by providing a degree of transparency to ...
متن کامل