KR101842681B1 - Visualization method and apparatus for large-scale biological network - Google Patents
Visualization method and apparatus for large-scale biological network Download PDFInfo
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- KR101842681B1 KR101842681B1 KR1020150086904A KR20150086904A KR101842681B1 KR 101842681 B1 KR101842681 B1 KR 101842681B1 KR 1020150086904 A KR1020150086904 A KR 1020150086904A KR 20150086904 A KR20150086904 A KR 20150086904A KR 101842681 B1 KR101842681 B1 KR 101842681B1
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Abstract
The present invention relates to a method and apparatus for automatically visualizing a large scale biological network. In more detail, the method and apparatus for visualizing a biological network including a plurality of nodes and a plurality of edges connecting each node, the method comprising the steps of: (S100) determining a connection state of the node based on edge list information input by a user; (S200) of recognizing the biological characteristics of the node based on the node list information inputted by the user (S300), calculating the biological similarity between the nodes based on the biological characteristics of the node (S300) And computing coordinate information of the node based on the biological similarity between the nodes (S400) and visualizing the biological network based on the coordinate information (S500).
Description
The present invention relates to a method and apparatus for automatically visualizing a large scale biological network, and more particularly, to a method and apparatus for automatically locating nodes in a network based on the biological characteristics of each node, And a method and apparatus for sequential visualization.
A network is a kind of combinatorial structure composed of a series of dots (nodes) and a line connecting them (edges). And a biological network is a network in which elements (genes, proteins, metabolites, diseases) involved in or related to a living organism are organized as nodes and biological associations between them appear as edges. In this case, network visualization means a process of picturing the network when the configuration information of the network, that is, the information of the node and the edge, is given. The key to this visualization process is to determine the location of the nodes. Once the position of the node is determined, the edge position is determined automatically because it is the line connecting the node. Therefore, the present invention proposes a new method for automatically determining the position of a node.
If you configure the network type in this way, the next step will require various functions to make the network easier to view. In particular, when a large network is visualized, it is difficult for the observer to recognize the contents accurately because the number of nodes and edges included therein is very large. Therefore, the present invention proposes a method of evaluating each node, assigning importance, and visualizing the network hierarchically according to the priority score. Through this, users can enlarge and observe more and more detailed networks by enlarging from a visualized form, summarized even if they are huge networks.
The biological system of the human body is very complex, consisting of a large variety of materials and numerous interactions. To understand this complex and huge system as a whole, it is necessary to understand the components and their relationships at a glance. It is important to develop a technology that visualizes these biological systems in the form of networks and converts them into a form that is easy to analyze and observe. Now, however, there is no way to properly visualize these huge networks. Conventional techniques have been inconvenient for setting information on the location of a node irregularly and simply implementing a huge network on a plane. Therefore, the present invention aims to solve these problems by effectively visualizing a large-scale biological network.
The solution to the problem of the present invention is not limited to those mentioned above, and other solutions not mentioned can be clearly understood by those skilled in the art from the following description.
According to an aspect of the present invention, there is provided a method of visualizing a biological network including a plurality of nodes and a plurality of edges connecting nodes, the method comprising the steps of: Identifying; Determining a biological characteristic of the node based on the node list information input by the user; Calculating biological similarities between the nodes based on the biological characteristics of the nodes; Calculating coordinate information of the node based on the connection state of the node and the biological similarity between the nodes; And visualizing the biological network based on the coordinate information.
The step of calculating coordinate information of the node may further include: calculating a relative distance between the plurality of nodes; And calculating a coordinate value through a Multi-Dimensional Scaling algorithm based on the distance.
The step of calculating the relative distance between the plurality of nodes may be performed through a calculation algorithm based on the biological similarity information between the nodes and the connection state information between the nodes.
In another aspect of the present invention, there is provided a method of visualizing a biological network including a plurality of nodes and a plurality of edges connecting the nodes, the method comprising: grasping a connection state of the node based on edge list information input by a user; Determining a biological characteristic of the node based on the node list information input by the user; Calculating a centrality of the node based on the connection state of the node; Calculating the importance of the node based on the biological characteristics of the node and the centrality of the node; Layering the nodes based on the importance; And prioritizing and visualizing the nodes sequentially based on the layering.
The present invention also provides a visualization apparatus for a biological network including a plurality of nodes and a plurality of edges connecting the nodes, the visualization apparatus comprising: a first calculation unit for determining a connection state of the node based on edge list information input by a user; A second calculation unit for determining a biological characteristic of the node based on the node list information input by the user; A third computing unit for computing a biological similarity between the nodes based on the biological characteristics of the node; A fourth computation unit for computing coordinate information of the node based on the connection state of the node and the biological similarity between the nodes, and a first output unit for visualizing the biological network based on the coordinate information.
The fourth calculation unit for calculating the coordinate information of the node may further include a 4-1 calculation unit for calculating a relative distance between the plurality of nodes and a 4-1 calculation unit for calculating a coordinate value through a Multi-Dimensional Scaling algorithm based on the distance 4-2 calculation unit.
The 4-1 calculation unit for calculating a relative distance between the plurality of nodes may be calculated through a calculation algorithm based on biological similarity information between the nodes and connection state information between the nodes.
The present invention also provides a visualization apparatus for a biological network including a plurality of nodes and a plurality of edges connecting the nodes, the visualization apparatus comprising: a first computing unit for determining a connection state of the node based on edge list information input by a user; A second calculation unit for determining biological characteristics of the node based on the inputted node list information, a fifth calculation unit for calculating the centrality of the node based on the connection state of the node, A seventh computing unit for layering the nodes based on the importance, and a second outputting unit for prioritizing and visualizing the nodes sequentially based on the layering, can do.
The present invention proposes a method and apparatus for automatically visualizing a large scale biological network. Conventional techniques have been inconvenient for setting information on the location of a node irregularly and simply implementing a huge network on a plane. By effectively visualizing large-scale biological networks, these problems can be solved and researchers can learn the information contained in the network efficiently.
The effects of the present invention are not limited to those mentioned above, and other effects not mentioned may be clearly understood by those skilled in the art from the following description.
1 is a flowchart showing a method of automatically determining and visualizing a node position according to the present invention.
2 is a graph illustrating an example of determining and visualizing node locations according to the present invention.
FIG. 3 is a flowchart showing a hierarchical visualization method of determining importance of nodes according to the present invention.
FIG. 4 is a diagram illustrating a method of hierarchically visualizing a node according to an exemplary embodiment of the present invention.
5 is a flowchart illustrating a method for automatically determining and visualizing node locations according to the present invention.
FIG. 6 is a flowchart showing a method of hierarchically visualizing a node according to the present invention.
Fig. 7 is a configuration diagram showing an apparatus for automatically determining and visualizing a node position according to the present invention.
FIG. 8 is a block diagram showing an apparatus for hierarchically visualizing nodes according to the present invention.
Hereinafter, preferred embodiments of a method and apparatus for automatically visualizing a large-scale biological network according to the present invention will be described in detail with reference to the accompanying drawings. In the drawings, the same reference numerals are used to designate the same or similar components throughout the drawings. In the following description of the present invention, a detailed description of known functions and configurations incorporated herein will be omitted when it may make the subject matter of the present invention rather unclear.
Referring to FIGS. 1 to 8, the present invention consists of the following two core methods, and there are essential elements for carrying out each method. At this time, it is assumed that the information about the network itself (node type and edge list) is generated as an input value from the user and already exists.
1 and 5 are flowcharts illustrating a method for automatically determining and visualizing a node position, which is the first method according to the present invention.
A method of visualizing a biological network including a plurality of nodes and a plurality of edges connecting each node, the method comprising the steps of: determining a connection state of a node based on edge list information input by a user (S100) (S300) of calculating a biological similarity between the nodes based on the biological characteristics of the node based on the biological information of the node based on the list information, determining a biological characteristic of the node based on the connection state of the node and the biological similarity between the nodes Calculating coordinate information (S400), and visualizing the biological network based on the coordinate information (S500).
In addition, calculating the coordinate information of the node includes calculating a relative distance between the plurality of nodes (S410) and calculating a coordinate value through a Multi-Dimensional Scaling algorithm based on the distance (S420).
The step S410 of calculating the relative distance between the plurality of nodes is performed through a calculation algorithm based on the biological similarity information between the nodes and the connection state information between the nodes.
In this case, the connection state between the nodes indicates whether the two nodes are connected or not, and is obtained by converting the edge list information inputted by the user.
In addition, biological characteristics information (biological functions, molecular functions, and intracellular locations) of nodes are obtained from various kinds of public databases (NCBI, HMDB, ONIM, etc.). The information in these databases is organized as a single integrated code (eg GO00101) rather than a generic word (eg, photosynthesis), and a Gene Ontology database is used to assign code to each word in this process.
In addition, the biological similarity information calculation algorithm between nodes can calculate the biological similarity between two nodes by using an algorithm that compares the biological characteristics information of the nodes based on the information of the biological characteristics of the nodes. In this case, the algorithm used is GoSemSim.
2 is a diagram illustrating an embodiment in which nodes are formed at corresponding positions based on position information generated through each step of a method of automatically determining and visualizing node positions.
Fig. 7 is a configuration diagram showing an apparatus for automatically determining and visualizing a node position according to the present invention. A visualization apparatus for a biological network including a plurality of nodes and a plurality of edges connecting each node, the visualization apparatus comprising: a first calculation unit (100) for grasping a connection state of the node based on edge list information input by a user; A
The fourth calculation unit for calculating the coordinate information of the node may include a 4-1
Also, the 4-1
FIGS. 3 and 6 are flowcharts illustrating a method of hierarchically visualizing nodes according to the present invention.
A method of visualizing a biological network including a plurality of nodes and a plurality of edges connecting each node, the method comprising the steps of: (S100) determining a connection state of the node based on edge list information input by a user (S100) (S200) of determining the biological characteristics of the node based on the node list information, calculating the centroid of the node based on the connection state of the node (S600), determining the importance of the node based on the biological characteristics of the node and the centroid of the node (S800) of layering the nodes based on the importance, and step S900 of sequentially prioritizing and visualizing the nodes based on the layering.
At this time, the centrality of the node is a measure of how much the node plays a key role in the network. The centrality includes Degree Centrality, Betweenness Centrality, and Closeness Centrality. These numbers are calculated using Mathematica based on the edge information.
The importance of a node is calculated by using a computation algorithm based on the information of the biological characteristics of the node and the centroid information of the node.
FIG. 4 is a diagram illustrating a method of hierarchically visualizing a node according to an exemplary embodiment of the present invention. Once the importance of the node is determined, it can be seen that each node of the network is layered with significance added to the coordinates. When the network is viewed as a whole (in a collapsed state), only a limited number of nodes having high importance are visualized preferentially in the network. When the user enlarges a specific area, the corresponding area is displayed on the screen, and the nodes in the area are visualized again in the order of importance, as many as the number of nodes excluded from the area.
Assuming that the importance level of the third step is applied to the network as shown in FIG. 4, in a state in which the user does not magnify, the entire area a of the screen is viewed. In this case, only the white nodes are selectively visualized. When looking at the area b, the white node and the hatched node are visualized. When the area is further enlarged and the area c is viewed, all the nodes are visualized. In actual implementation, the nodes are not distinguished step by step, but only a specified number of nodes are automatically visualized in order of importance from the nodes present on the screen viewed by the current user.
FIG. 8 is a block diagram showing an apparatus for hierarchically visualizing nodes according to the present invention. A visualization apparatus for a biological network including a plurality of nodes and a plurality of edges connecting each node, the visualization apparatus comprising: a first calculation unit (100) for grasping a connection state of the node based on edge list information input by a user; A
The foregoing description is merely illustrative of the technical idea of the present invention, and various changes and modifications may be made by those skilled in the art without departing from the essential characteristics of the present invention. Therefore, the embodiments disclosed in the present invention are intended to illustrate rather than limit the scope of the present invention, and the scope of the technical idea of the present invention is not limited by these embodiments. The scope of protection of the present invention should be construed according to the following claims, and all technical ideas within the scope of equivalents should be construed as falling within the scope of the present invention.
100: first calculation unit 200: second calculation unit
300: third calculating section 400: fourth calculating section
410: 4-1 calculation unit 420: 4-2 calculation unit
500: output unit 600: fifth calculation unit
700: sixth calculation section 800: seventh calculation section
900: second output section
Claims (8)
(S100) of grasping the connection state of the node based on the edge list information input by the first outputting unit of the visualization apparatus of the biological network by the user;
(S200) of recognizing the biological characteristics of the node based on the node list information input by the second computing unit of the visualization apparatus by the user;
(S300) of calculating a biological similarity between the nodes based on the biological characteristics of the node, wherein the third calculation unit of the visualization apparatus calculates the biological similarity between the nodes;
(S400) of calculating coordinate information of the node based on a connection state of the node and a biological similarity between the nodes, wherein the fourth calculation unit of the visualization apparatus calculates (S400) coordinate information of the node;
Visualizing the biological network based on the coordinate information, wherein the first outputting unit of the visualization unit (S500) comprises:
Calculating a center of gravity of the node based on a connection state of the node, the fifth calculation unit of the visualization apparatus (S600);
Calculating (S700) the importance of the node based on the biological characteristic of the node and the centrality of the node;
The seventh calculating unit of the visualization apparatus layering the nodes based on the importance (S800); And
(S900) of prioritizing and sequentially visualizing the nodes based on the layering, wherein the second outputting unit of the visualization unit sequentially visualizes the nodes;
The method comprising the steps of:
The step (S400) of calculating coordinate information of the node
Calculating a relative distance between the plurality of nodes (S410); And
Calculating a coordinate value through a Multi-Dimensional Scaling algorithm based on the distance (S420);
The method comprising the steps of:
Wherein the calculating the relative distance between the plurality of nodes comprises:
Wherein the computation algorithm is based on biological similarity information between the nodes and connection state information between the nodes.
A first calculation unit (100) for grasping a connection state of the node based on edge list information input by a user;
A second calculation unit (200) for grasping the biological characteristics of the node based on the node list information input by the user;
A third calculation unit (300) for calculating a biological similarity between the nodes based on biological characteristics of the node;
A fourth calculation unit (400) for calculating coordinate information of the node based on the connection state of the node and the biological similarity between the nodes;
A first output unit (500) for visualizing the biological network based on the coordinate information;
A fifth calculation unit 600 for calculating the center of gravity of the node based on the connection state of the node;
A sixth calculation unit 700 for calculating the importance of the node based on the biological characteristic of the node and the centrality of the node;
A seventh calculator 800 for layering the nodes based on the importance; And
A second output unit 900 for prioritizing and sequentially visualizing the nodes based on the layering;
And a visualization unit for visualizing the biological network.
The fourth calculation unit 400, which calculates coordinate information of the node,
A 4-1 calculation unit (410) for calculating a relative distance between the plurality of nodes; And
A fourth-2 calculator 420 for calculating a coordinate value through a Multi-Dimensional Scaling algorithm based on the distance;
And a visualization unit for visualizing the biological network.
The 4-1 calculation unit 410 for calculating a relative distance between the plurality of nodes,
And computing connection information between the nodes through the calculation algorithm based on the biological similarity information between the nodes and the connection state information between the nodes.
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| Adai, A T. ‘LGL: Creating a map of protein function with an algorithm for visualizing very large biological networks’, Journal of Molecular Biology, 340(1), pp. 179-190 (2004. 6. 25. 공개) |
| Gibson, H. ‘A survey of two-dimensional graph layout techniques for information visualisation. Information Visualization’ 12(3-4). pp. 324-357 (2012. 9. 5. 공개) |
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