437 research outputs found

    MIANN models in medicinal, physical and organic chemistry

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    [Abstract] Reducing costs in terms of time, animal sacrifice, and material resources with computational methods has become a promising goal in Medicinal, Biological, Physical and Organic Chemistry. There are many computational techniques that can be used in this sense. In any case, almost all these methods focus on few fundamental aspects including: type (1) methods to quantify the molecular structure, type (2) methods to link the structure with the biological activity, and others. In particular, MARCH-INSIDE (MI), acronym for Markov Chain Invariants for Networks Simulation and Design, is a well-known method for QSAR analysis useful in step (1). In addition, the bio-inspired Artificial-Intelligence (AI) algorithms called Artificial Neural Networks (ANNs) are among the most powerful type (2) methods. We can combine MI with ANNs in order to seek QSAR models, a strategy which is called herein MIANN (MI & ANN models). One of the first applications of the MIANN strategy was in the development of new QSAR models for drug discovery. MIANN strategy has been expanded to the QSAR study of proteins, protein-drug interactions, and protein-protein interaction networks. In this paper, we review for the first time many interesting aspects of the MIANN strategy including theoretical basis, implementation in web servers, and examples of applications in Medicinal and Biological chemistry. We also report new applications of the MIANN strategy in Medicinal chemistry and the first examples in Physical and Organic Chemistry, as well. In so doing, we developed new MIANN models for several self-assembly physicochemical properties of surfactants and large reaction networks in organic synthesis. In some of the new examples we also present experimental results which were not published up to date.Ministerio de Ciencia e Innovación; CTQ2009-07733Universidad del Pais Vasco; UFI11/22Universidad del Pais Vasco; GIU 094

    Operationally meaningful representations of physical systems in neural networks

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    To make progress in science, we often build abstract representations of physical systems that meaningfully encode information about the systems. The representations learnt by most current machine learning techniques reflect statistical structure present in the training data; however, these methods do not allow us to specify explicit and operationally meaningful requirements on the representation. Here, we present a neural network architecture based on the notion that agents dealing with different aspects of a physical system should be able to communicate relevant information as efficiently as possible to one another. This produces representations that separate different parameters which are useful for making statements about the physical system in different experimental settings. We present examples involving both classical and quantum physics. For instance, our architecture finds a compact representation of an arbitrary two-qubit system that separates local parameters from parameters describing quantum correlations. We further show that this method can be combined with reinforcement learning to enable representation learning within interactive scenarios where agents need to explore experimental settings to identify relevant variables.Comment: 24 pages, 13 figure

    ResMGCN: Residual Message Graph Convolution Network for Fast Biomedical Interactions Discovering

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    Biomedical information graphs are crucial for interaction discovering of biomedical information in modern age, such as identification of multifarious molecular interactions and drug discovery, which attracts increasing interests in biomedicine, bioinformatics, and human healthcare communities. Nowadays, more and more graph neural networks have been proposed to learn the entities of biomedical information and precisely reveal biomedical molecule interactions with state-of-the-art results. These methods remedy the fading of features from a far distance but suffer from remedying such problem at the expensive cost of redundant memory and time. In our paper, we propose a novel Residual Message Graph Convolution Network (ResMGCN) for fast and precise biomedical interaction prediction in a different idea. Specifically, instead of enhancing the message from far nodes, ResMGCN aggregates lower-order information with the next round higher information to guide the node update to obtain a more meaningful node representation. ResMGCN is able to perceive and preserve various messages from the previous layer and high-order information in the current layer with least memory and time cost to obtain informative representations of biomedical entities. We conduct experiments on four biomedical interaction network datasets, including protein-protein, drug-drug, drug-target, and gene-disease interactions, which demonstrates that ResMGCN outperforms previous state-of-the-art models while achieving superb effectiveness on both storage and time.Comment: In progres
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