论文标题

Chemoverse:新分子发现潜在空间的歧管遍历

ChemoVerse: Manifold traversal of latent spaces for novel molecule discovery

论文作者

Singh, Harshdeep, McCarthy, Nicholas, Ain, Qurrat Ul, Hayes, Jeremiah

论文摘要

为了设计一个更有效,更有效的化学实体,必须鉴定具有所需化学特性的分子结构。使用神经网络和机器学习的生成模型的最新进展正在该领域的许多新兴初创公司和研究人员广泛使用,以设计类似药物的化合物的虚拟库。尽管这些模型可以帮助科学家迅速产生新的分子结构,但挑战仍然存在于对生成模型的潜在空间的智能探索中,从而降低了生成过程中的随机性。在这项工作中,我们通过启发式搜索介绍了一种多种遍历,以探索潜在的化学空间。可以纳入不同的启发式方法和得分,例如Tanimoto系数,合成可及性,结合活性和QED药物务实,以提高生成分子的所需分子特性的有效性和接近度。为了评估流形遍历探索,我们使用各种生成模型(如语法变异自动编码器)(有和不引起注意)生成潜在的化学空间,因为它们处理化合物的随机产生和有效性。通过这种新颖的遍历方法,我们能够在潜在空间中找到更多看不见的化合物和更具体的区域。最后,这些组件在一个简单的平台中聚集在一起,使用户可以执行新颖生成化合物的搜索,可视化和选择。

In order to design a more potent and effective chemical entity, it is essential to identify molecular structures with the desired chemical properties. Recent advances in generative models using neural networks and machine learning are being widely used by many emerging startups and researchers in this domain to design virtual libraries of drug-like compounds. Although these models can help a scientist to produce novel molecular structures rapidly, the challenge still exists in the intelligent exploration of the latent spaces of generative models, thereby reducing the randomness in the generative procedure. In this work we present a manifold traversal with heuristic search to explore the latent chemical space. Different heuristics and scores such as the Tanimoto coefficient, synthetic accessibility, binding activity, and QED drug-likeness can be incorporated to increase the validity and proximity for desired molecular properties of the generated molecules. For evaluating the manifold traversal exploration, we produce the latent chemical space using various generative models such as grammar variational autoencoders (with and without attention) as they deal with the randomized generation and validity of compounds. With this novel traversal method, we are able to find more unseen compounds and more specific regions to mine in the latent space. Finally, these components are brought together in a simple platform allowing users to perform search, visualization and selection of novel generated compounds.

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