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36 results about "Molecular graph" patented technology

In chemical graph theory and in mathematical chemistry, a molecular graph or chemical graph is a representation of the structural formula of a chemical compound in terms of graph theory. A chemical graph is a labeled graph whose vertices correspond to the atoms of the compound and edges correspond to chemical bonds. Its vertices are labeled with the kinds of the corresponding atoms and edges are labeled with the types of bonds. For particular purposes any of the labelings may be ignored.

Self-supervised graph neural network pre-training method based on comparative learning

The invention relates to a self-supervised graph neural network pre-training method based on comparative learning. The method comprises the steps of carrying out preprocessing on compound molecules of a public database, and screening out organic molecules; performing structural decomposition and extraction on the screened organic molecules, taking the obtained substructures as identifiers, and constructing a corpus of the substructures; taking the decomposed substructures as super nodes, and constructing corresponding subgraph data, wherein the subgraph data and the original molecular graph data form positive sample pairs, and a plurality of subgraph data are randomly selected to form negative sample pairs with the original molecular graph data; constructing a graph convolutional neural network based on an attention mechanism, and forming a self-supervised learning model based on a multi-level gating circulation unit and a multi-layer perceptron module; and inputting all positive and negative sample pair data into the self-supervised learning model for pre-training and storing, thereby facilitating fine adjustment of downstream tasks. The problem of insufficient generalization performance generated by deep learning model training in a scene lacking labeled drug molecules is solved.
Owner:JINAN UNIVERSITY

Method and apparatus for molecular toxicity prediction based on multi-task graph neural network

The invention discloses a method and an apparatus for molecular toxicity prediction based on a multi-task graph neural network. The method comprises the following steps: S1, preparing a toxicity data set, and obtaining toxicity data represented by a chemical molecule standard expression; S2, generating an atomic node eigenvector by using the toxicity data which is obtained in the step S1 and represented by the chemical molecule standard expression; S3, generating a side information eigenvector by using the toxicity data which is obtained in the step S1 and represented by the chemical molecule standard expression; S4, on the basis of the atomic node eigenvector obtained in the step S2 and the side information eigenvector obtained in the step S3, constructing a molecular toxicity prediction model based on a multi-task graph neural network; S5, verifying performance of the model. According to the multi-task graph neural network designed for molecular toxicity datasets, an automatic learning molecular graph structure information model is constructed, and the performance of a toxicity prediction task can be improved by using a multi-task learning method in combination with the relevance between molecular toxicity tasks.
Owner:NANJING UNIV OF POSTS & TELECOMM

Novel deep learning model for predicting compound protein affinity, computer equipment and storage medium

The invention discloses a novel deep learning model for predicting compound protein affinity. The novel depth model comprises a BiGRU (Bipolar Gated Recirculation Unit) model, a GCN (Graph Convolutional Neural Network) model and a CNN (Convolutional Neural Network) model, wherein the whole network architecture is BiGRU/BiGRU/GCN-CNN. The bidirectional gating cycle unit model comprises a sequence processing model composed of two gating cycle units (GRU), one input is forward input, the other input is reverse input, and the bidirectional gating cycle unit model is a bidirectional recurrent neural network with only an input gate and a forgetting gate. The input of the model is a compound one-dimensional SMILES sequence, a protein sequence and a compound two-dimensional molecular diagram, andthe three sequences are respectively input into a BiGRU/BiGRU/GCN model. BiGRU/BiGRU/GCN output represents a feature vector of the compound and a feature vector of the protein. The CNN model is composed of a convolution layer, a pooling layer and a full connection layer, and inputs of the model are a feature vector of a compound and a feature vector of a protein; The final output of the BiGRU/BiGRU/GCN-CNN model is a root mean square error value for predicting a compound protein affinity value.
Owner:CHINA UNIV OF PETROLEUM (EAST CHINA)

Small molecule drug hERG toxicity prediction method and device based on graph attention mechanism transfer learning

ActiveCN113192571AImprove performancePredictive attribute value contributes a lotChemical property predictionMolecular designData setAlgorithm
The invention discloses a graph attention mechanism transfer learning-based small molecule drug hERG toxicity prediction method and device; the method comprises the following steps: S1, data set preprocessing: enabling a to-be-detected drug-like compound to generate a fingerprint sequence through molecular fingerprint generation software; s2, acquiring atom and chemical bond characteristics through the fingerprint sequence generated in the step S1, and constructing a molecular graph and graph characteristics through the atom and chemical bond characteristics; s3, processing the molecular map obtained in the step S2 through a map attention mechanism, and generating a feature vector of each atom in the molecule; s4, generating a molecular feature vector through a graph attention mechanism and the feature of each atom. According to the method, a molecular graph structure is processed based on a graph attention mechanism, a substructure which contributes to a predicted attribute value is effectively obtained, and a source domain data set and a target domain data set are processed based on transfer learning; and thereby, the problem that the sample size is insufficient is effectively solved.
Owner:NANJING UNIV OF POSTS & TELECOMM

Drug small molecule property prediction method, device and equipment based on graph neural network

The invention discloses a drug small molecule property prediction method, device and equipment based on a graph neural network, relates to the technical field of artificial intelligence, and can solve the technical problems of low efficiency and low accuracy of drug small molecule property prediction at present. The method comprises the following steps: generating a molecular graph structure according to a chemical molecular structure of a target drug small molecule, and generating a molecular sub-graph structure according to a functional group intermediate structure of the target drug small molecule; determining a first feature vector corresponding to the molecular graph structure and a second feature vector corresponding to the molecular sub-graph structure by using a target graph neural network model; and constructing a third feature vector according to the first feature vector and the second feature vector, and inputting the third feature vector into a trained property prediction model to obtain a property prediction result of the target drug small molecule. The method is suitable for realizing intelligent prediction of drug micromolecule properties based on an artificial intelligence technology.
Owner:PING AN TECH (SHENZHEN) CO LTD

Article molecule generation method, device and equipment, and storage medium

The invention is suitable for the technical field of computer aided article design, and provides an article molecule generation method, device and equipment and a storage medium. The method comprisesthe following steps: inputting a first molecular diagram structure and a first connection tree structure of a source molecule into a molecule generation model, and encoding the first molecular diagramstructure and the first connection tree structure through the molecule generation model to obtain embedded representation of the source molecule; decoding based on the structure information of each substructure in the label set and the embedded representation to generate a second connection tree structure of the target molecule; and decoding the second connection tree structure to obtain a secondmolecular diagram structure of the target molecule. The structure information of each substructure in the tag set and the embedded representation of the source molecule are combined for decoding, sothat the structure information of each substructure in the tag set can be well utilized to predict the connection tree structure of the target molecule, the reasonability of the prediction result is improved, and the influence of tag imbalance is relieved.
Owner:SHENZHEN INST OF ADVANCED TECH

Drug and target interaction prediction method and device, equipment and storage medium

The invention relates to the technical field of neural networks of the artificial intelligence technology, and provides a drug and target interaction prediction method, device and equipment and a storage medium, and the method comprises the steps: calling a pre-constructed graph neural network to extract drug features in a molecular graph of a drug, processing the molecular map according to a restart random walk algorithm, predicting the similarity of drug characteristics between two adjacent nodes in the molecular map to obtain global structure information, inputting the global structure information into a preset deep neural network to obtain low-dimensional characteristic information of drugs, and obtaining a protein sequence of a target, and calling a long-short-term memory network to process the protein sequence to obtain protein features, and inputting the low-dimensional feature information and the protein features into a preset full-connection layer to predict an interaction result of the drug and the target so as to extract information contained in the drug and the protein sequence in a targeted manner. And the prediction efficiency of the interaction between the drug and the target is improved.
Owner:PING AN TECH (SHENZHEN) CO LTD

Molecular graph comparison learning method based on chemical element knowledge graph

The invention discloses a molecular graph comparison learning method based on a chemical element knowledge graph. The method comprises the following steps of: constructing a chemical element knowledge graph according to all chemical attributes of each chemical element in a periodic table of chemical elements; performing graph enhancement on the molecular graph by utilizing the chemical element knowledge graph to obtain a molecular enhancement graph; obtaining graph representations of the molecular graph and the molecular enhancement graph by using a pluggable representation model; adopting a hard negative sample mining technology to select other molecular graphs similar to the molecular graph in the molecular fingerprint space as negative samples; mapping the graph representation of positive sample pairs and the graph representation of negative sample pairs to the same space, constructing a contrast loss function by maximizing the consistency between the positive sample pairs and minimizing the consistency between the negative sample pairs, and performing optimization learning by using the contrast loss function; and forming a prediction model by using the parameter-determined pluggable representation model and a nonlinear classifier, and predicting the molecular properties of the molecular graph by using a parameter-finely-adjusted prediction model so as to improve the prediction accuracy of molecular properties.
Owner:ZHEJIANG UNIV

Intelligent prediction method for small molecule-protein binding affinity

PendingCN114333984ASolve the problem that it is difficult to quickly mine protein structure informationAccurate Sequence CharacterizationNeural architecturesNeural learning methodsAlgorithmTheoretical computer science
The invention provides a protein weight graph-based small molecule-protein binding affinity intelligent prediction method, which comprises the following steps of: firstly, constructing a small molecule graph based on SMILES, constructing a protein weight graph based on a sequence, and secondly, respectively extracting the characteristics of the small molecule graph and the protein weight graph by adopting two graph convolutional neural networks; and constructing a graph convolutional neural network to extract the features of the two, splicing the obtained feature vectors, and further predicting the affinity of the two. According to the protein weight graph constructed by the invention, more accurate representation of the sequence is realized, and the interaction among amino acid residues is more intuitively and effectively represented by a graph structure; the constructed protein weight graph does not need to be subjected to an extremely complex sequence alignment process, so that data processing is quicker, the method is suitable for a virtual screening process of a large molecular database, and more accurate small molecule-protein affinity prediction can be realized.
Owner:QINGDAO TECHNOLOGICAL UNIVERSITY

Directional molecule generation method based on graph neural network

PendingCN113140267AEnsure chemical validityMolecular designNeural architecturesAlgorithmGraph generation
The invention relates to a directed molecule generation method based on a graph neural network, and relates to the technical field of material molecules. Comprising the following steps: converting an organic molecular structure graph into a molecular graph in a topological mapping mode, and taking embedded representation of the molecular graph as input of a graph neural network model; through a graph neural network model, learning the molecular graphs based on a message propagation process, including representations of nodes and edges in the molecular graphs; the generated representations are learned through a graph neural network so that various decisions can be made in the graph generation process; in the decision-making process, the new structure is added to the existing graph in a form conforming to the organic molecule chemical rule, and the probability of the addition event depends on the historical graph derivation process of the graph. The finally generated novel molecules are confirmed through chemical valence constraint, and the chemical effectiveness of the generated molecules can be ensured. According to the method, effective novel molecular structures with chemical properties similar to those of original molecules can be generated aiming at an organic molecule database.
Owner:BEIJING UNIV OF CHEM TECH

Data-mechanism driven material attribute prediction method of graph neural network

The invention discloses a data-mechanism driven material attribute prediction method of a graph neural network. The method comprises the following steps: S1, obtaining descriptor features and a graph structure of a to-be-predicted material molecule; s2, a final feature descriptor is screened out through feature engineering; s3, using graph convolution and a graph attention network to extract different levels of molecular graph features; s4, fusing the molecular graph features with the descriptor features by using a feature fusion layer; s5, using a correction module to better fuse the calculated value and the experimental value; wherein the calculated value is a numerical value obtained through simulation calculation according to a first principle, and the experimental value is an actual material attribute measured through an experiment; and S6, fusing the calculated value of the mechanism-driven model and the deep learning data-driven model for model reasoning, and outputting a numerical value of a prediction attribute. According to the method, descriptor features of molecules and graph structure features are fused, and the problems that graph structure data information is incomplete and molecular attributes are ignored by the descriptor features are solved.
Owner:UNIV OF SCI & TECH BEIJING

Drug molecule property prediction method, device and equipment based on comparative learning

The invention discloses a drug molecule property prediction method, device and equipment based on comparative learning, relates to the technical field of artificial intelligence, and can solve the technical problems of low efficiency and poor prediction performance of drug molecule property prediction at present. Comprising the following steps: generating a target molecular map structure of a target drug molecule according to a chemical molecular structure, and generating a target three-dimensional conformation of the target drug molecule; using the trained graph neural network model to determine a first feature vector corresponding to the target molecular graph structure; a second feature vector corresponding to the target three-dimensional conformation is determined through a trained convolutional neural network model, and the graph neural network model and the convolutional neural network model are obtained through comparative learning and joint training of a positive sample pair and a negative sample pair; and constructing a third feature vector according to the first feature vector and the second feature vector, and inputting the third feature vector into the trained property prediction model to obtain a property prediction result of the target drug molecule.
Owner:PING AN TECH (SHENZHEN) CO LTD

Software defect discovery method based on regional molecular graph mining

The invention provides a software defect discovery method based on regional molecular graph mining, and relates to the technical field of software engineering. The method comprises the following steps: firstly, extracting software packages of a new version and an old version from a software project, performing same data preprocessing on the software packages of the new version and the old version,constructing a control flow graph of a program, and storing the control flow graph into a text file to obtain a positive graph data set and a negative graph data set; performing hash conversion on the program statements stored in the control flow diagram of the text file, so that the control flow diagram is represented by numerical values obtained after Hash conversion of the program statements;carrying out overlay mining on the obtained hash-converted positive and negative graph data sets to obtain an overlay graph set; performing data vectorization on the control flow graphs in the positive and negative graph data sets according to the coverage graph set; and training an extreme learning machine by taking the control flow diagram subjected to data vectorization as feature training data, obtaining a training model by adopting a voting mechanism, and testing a to-be-tested program file through the tested training model to discover software defects.
Owner:NORTHEASTERN UNIV

Training method and device of molecular graph reconstruction model and electronic equipment

The invention provides a molecular graph reconstruction model training method and device and electronic equipment, the method is suitable for the artificial intelligence medicine field, and the molecular graph reconstruction model comprises an encoder, a decoder and a graph matching module; in the training method provided by the invention, on one hand, a graph matching module is designed as a pre-training module, and a relation matrix output by the graph matching module is designed to be used for calculating the reconstruction loss between a sample molecular graph and a reconstruction molecular graph, on the other hand, a representation vector of the sample molecular graph output by an encoder is designed as an input vector of a decoder, and the reconstruction loss between the sample molecular graph and the reconstruction molecular graph is calculated. According to the molecular graph reconstruction model training method provided by the invention, the molecular graph reconstruction model can be suitable for a molecular discovery process, the matching complexity and resource consumption can be reduced, the matching accuracy is improved, and the guiding effect of a graph matching module on the molecular graph reconstruction model is further improved. In addition, the method provided by the invention can also improve the practicability and reconstruction effect of the molecular graph reconstruction model.
Owner:TENCENT TECH (SHENZHEN) CO LTD
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