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تسجيل مستخدم جديدMolecular Design Based on Artificial Neural Networks, Integer Programming and Grid Neighbor Search
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A novel framework has recently been proposed for designing the molecular structure of chemical compounds with a desired chemical property using both artificial neural networks and mixed integer linear programming. In the framework, a chemical graph with a target chemical value is inferred as a feasible solution of a mixed integer linear program that represents a prediction function and other requirements on the structure of graphs. In this paper, we propose a procedure for generating other feasible solutions of the mixed integer linear program by searching the neighbor of output chemical graph in a search space. The procedure is combined in the framework as a new building block. The results of our computational experiments suggest that the proposed method can generate an additional number of new chemical graphs with up to 50 non-hydrogen atoms.
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Analysis of chemical graphs is a major research topic in computational molecular biology due to its potential applications to drug design. One approach is inverse quantitative structure activity/property relationship (inverse QSAR/QSPR) analysis, whi
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Recently a novel framework has been proposed for designing the molecular structure of chemical compounds using both artificial neural networks (ANNs) and mixed integer linear programming (MILP). In the framework, we first define a feature vector $f(C
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Molecular machine learning bears promise for efficient molecule property prediction and drug discovery. However, due to the limited labeled data and the giant chemical space, machine learning models trained via supervised learning perform poorly in g
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Nearest neighbor search has found numerous applications in machine learning, data mining and massive data processing systems. The past few years have witnessed the popularity of the graph-based nearest neighbor search paradigm because of its superior
ity over the space-partitioning algorithms. While a lot of empirical studies demonstrate the efficiency of graph-based algorithms, not much attention has been paid to a more fundamental question: why graph-based algorithms work so well in practice? And which data property affects the efficiency and how? In this paper, we try to answer these questions. Our insight is that the probability that the neighbors of a point o tends to be neighbors in the KNN graph is a crucial data property for query efficiency. For a given dataset, such a property can be qualitatively measured by clustering coefficient of the KNN graph. To show how clustering coefficient affects the performance, we identify that, instead of the global connectivity, the local connectivity around some given query q has more direct impact on recall. Specifically, we observed that high clustering coefficient makes most of the k nearest neighbors of q sit in a maximum strongly connected component (SCC) in the graph. From the algorithmic point of view, we show that the search procedure is actually composed of two phases - the one outside the maximum SCC and the other one in it, which is different from the widely accepted single or multiple paths search models. We proved that the commonly used graph-based search algorithm is guaranteed to traverse the maximum SCC once visiting any point in it. Our analysis reveals that high clustering coefficient leads to large size of the maximum SCC, and thus provides good answer quality with the help of the two-phase search procedure. Extensive empirical results over a comprehensive collection of datasets validate our findings.
A novel framework has recently been proposed for designing the molecular structure of chemical compounds with a desired chemical property using both artificial neural networks and mixed integer linear programming. In this paper, we design a new metho
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