What's new in DiscretePath 2.6.5
Apr 30, 2024
- Improvements:
- Both the clustering on ‘Hitting time’ and ‘Nearest neighbor’ are standardized for the order of the vertices from which the clustering is started. This makes the clustering less sensitive to the way the graph was constructed.
- Clustering via ‘Hitting time’ has been made more efficient, although clustering larger graphs can still take a long time.
- Bug fixes:
- The presence of self-loops does not interfere with clustering based on either ‘Hitting time’ and ‘Nearest neighbor’.
- Memory usage when calculating clusters has been optimized.
New in DiscretePath 2.6.4 (Apr 29, 2024)
- Improvements:
- Both the clustering on ‘Hitting time’ and ‘Nearest neighbor’ are standardized for the order of the vertices from which the clustering is started. This makes the clustering less sensitive to the way the graph was constructed.
- Clustering via ‘Hitting time’ has been made more efficient, although clustering larger graphs can still take a long time.
New in DiscretePath 2.6.3 (Apr 5, 2024)
- Bug fix:
- A bug in the clustering algorithms has been fixed.
New in DiscretePath 2.6.1 (Mar 11, 2024)
- Improvements:
- A new effective clustering method based on the ‘hitting time distribution’ of the vertices has been added.
- The ‘nearest neighbor’ clustering method has been updated.
- Bug fixes:
- The help window that appears when connecting two vertices with an edge is correctly positioned at the mouse pointer.
- The error window that sometimes appears after closing the application no longer appears (MacOS).
New in DiscretePath 2.5.6 (Mar 1, 2024)
- Improvements:
- ‘Help info’ updated.
- Added AI for calculating cliques and centralities.
- Bug fixes:
- Corrected clustering with ‘Take weight of edges into account’ when vertices connected by edges with lower weights have stronger clustering.
New in DiscretePath 2.5.4 (Feb 21, 2024)
- Improvements:
- For complex graphs, constructing a random walk with a start and end vertex is much faster.
- Listing the vertices or edges in the ‘Info tab’ of the Palette window can be canceled with the ‘ESC’ key.
- When the orientation of an edge is changed in the ‘Layout tab’ of the Palette window, the change is visualized in real time in the canvas.
- Bug fixes:
- No error message is displayed when the application is closed.
- When a random walk is not possible, the graph is not frozen.
New in DiscretePath 2.5.3 (Nov 25, 2023)
- Extract ('extract all') the downloaded zip file.
- The folder 'DiscretePath' that is created can be copied to a location on disk.
- P.S.: Preferentially to "C:/Program files" (to do this you need administrator rights on your computer).
New in DiscretePath 2.4.5 (Aug 24, 2023)
- Improvements:
- A.I. module: 'Decision tree'
- In the 'PaletteWindow' the choice is available to build a decision tree with one
- Or more numerical attributes and/or a numerical class, on a simplified or more
- Detailed level.
- Even if the data does not allow building a good model, a model is always produced.
- The user can then decide how to proceed.
- After building the model, a summary of the model's robustness is displayed in the
- 'Info tab' of the Palette window.
- Bug fixes:
- A.I. module: 'Decision tree'
- Missing data in the imported dataset can now be represented by any character in
- Addition to an empty field in the dataset.
- When data is missing from the imported dataset, the samples can be deleted or
- Kept. In the latter case, the missing data is replaced by imputation. In the previous
- Version, the replacement was not always complete. In this version, the imputation of
- The missing data is complete.
- In the previous version, invalid error messages could be displayed. This has been
- Fixed.
New in DiscretePath 2.4.4 (Aug 12, 2023)
- Missing data in the imported dataset can now be represented by any character in addition to an empty field in the dataset.
- When data is missing from the imported dataset, the samples can be deleted or kept. In the latter case, the missing data is replaced by imputation. In the previous version, the replacement was not always complete. In this version, the imputation of the missing data is complete.
- In the previous version, invalid error messages could be displayed. This has been fixed.
New in DiscretePath 2.4.3 (Aug 12, 2023)
- Bug fixes for A.I. module: ‘Decision tree’:
- Missing data in the imported dataset can now be represented by any character in addition to an empty field in the dataset.
- When data is missing from the imported dataset, the samples can be deleted or kept. In the latter case, the missing data is replaced by imputation. In the previous version, the replacement was not always complete. In this version, the imputation of the missing data is complete.
- In the previous version, invalid error messages could be displayed. This has been fixed.
New in DiscretePath 2.4.1 (Aug 8, 2023)
- This version contains an important update for the 'Decision tree' module.
- The processing of numerical data has been highly optimized.
- The import of inconsistent data is handled efficiently.
New in DiscretePath 2.4.0 (Jul 27, 2023)
- Improvements:
- An 'Artificial Intelligence' module has been added ('A.I.' tab of the Palette window). This module covers A.I. algorithms that use graphs in some form. This release includes the first supervised learning A.I. algorithms: "Decision Trees". The decision tree algorithms can handle both categorical and numerical data and can be used for both classification and regression tasks.
- Bug fixes:
- 'Random walks' now works with directed graphs and no errors occur when using edge weight as a walk parameter.
New in DiscretePath 2.3.0 (Feb 16, 2023)
- Vertices can be organized in groups (improves graph layout, visualization and analysis).
- Vertices can be organized in sub and super categories.
- X,Y-coordinates of the vertices can be imported. For example, this way the vertices that represent locations on a map can be set to their latitude and longitude coordinates.
- Calculation of the ‘maximum clique’ and ‘all cliques’. The maximum clique is used in many applications to identify the most connected and interactive parts in biological, collaboration, interaction, technological, social, ….. networks. The identification of all cliques allows to identify also the smaller interactive parts of a network. For the calculation of ‘all cliques’ a lower limit can be set (minimum number of vertices that the clique must contain). If a graph contains multiple maximum cliques, ‘all cliques’ allows them to be identified.
New in DiscretePath 2.2.14 (Feb 3, 2023)
- Important bug fix:
- The import of x,y coordinates of vertices:
- File -> Import graph data from clipboard -> x,y coordinates of vertices
- is no longer sensitive to the thousands and decimal separators set in the 'Operating System Settings'.
- Previously, only numbers with a space or without a thousands separator and a dot as a decimal separator were accepted.
New in DiscretePath 2.2.11 (Jan 4, 2023)
- Improvements:
- Optimization of ‘Undo/Redo’.
- Optimization of interactivity of the table in the ‘Info’ tab with the graph in the canvas.
- Bug fixes:
- When data was added to a graph using the ‘Import into the current graph’ menu item and most of the data was identical to the current graph, an exception could occur and if a ‘list of edges’ was imported the identical edges were duplicated. Both points have been resolved.
New in DiscretePath 2.2.9 (Oct 14, 2022)
- Improvements:
- DiscretePathPLUS: Calculation of the ‘maximum clique’ and ‘all cliques’. The maximum clique is used in many applications to identify the most connected and interactive parts in biological, collaboration, interaction, technological, social, ….. networks. The identification of all cliques allows to identify also the smaller interactive parts of a network. For the calculation of ‘all cliques’ a lower limit can be set (minimum number of vertices that the clique must contain). If a graph contains multiple maximum cliques, ‘all cliques’ allows them to be identified.
- A menu item is added to the menu bar to reset all edges of a graph to their default color: “Edit” -> “Set all edges to the default color”. This can be useful if, for example, after the calculation of the edge betweenness or the maximum clique, the graph has been saved and the user wants to delete the results afterwards.
- Bug fixes:
- DiscretePathPLUS: In versions 2.2.7 and 2.2.8, when the XY coordinates of the vertices were imported, the graph was not drawn correctly. There was an error in scaling, this has now been corrected.
New in DiscretePath 2.2.8 (Oct 11, 2022)
- Bug fix for the Windows version:
- In previous versions, when DiscretePath was restarted after a crash, the window with the option to reopen the graph that was being edited or analyzed at the time of the crash was hidden behind the main window. In this version, the main window is now minimized so that the ‘options window’ is visible.
New in DiscretePath 2.2.7 (Aug 9, 2022)
- Improvements:
- Importing data from the clipboard is 2 to 3 times faster.
- Opening a ‘.gdp’ file is 2 times faster.
- When the vertices are drawn in the layout of the categories to which they belong, the legend of the categories is displayed. The legend can be copied and printed.
- The graph layout algorithms have been modified for faster drawing.
- Bug fixes:
- Adding data to a graph using the clipboard no longer interferes with the selection of edges in the resulting composite graph.
- Adding data to a graph can now use an adjacency matrix without a row and column header.
- When changing the gray color of the edges, the newly drawn edges will have the set color (in the previous versions, the newly drawn edges were always black).
- DiscretePathPLUS: Manually drawing an edge to or from a group vertex is not allowed. The edges to or from a group vertex represent edges from or to the vertices that are part of the group vertex to vertices outside the group vertex to which they belong.
New in DiscretePath 2.2.6 (Jul 21, 2022)
- Bug fixes:
- For Mac only: The main window is now located just below the menubar of the Mac computers with Apple silicon that features a notch.
- The contents of a cell of the table in the ‘info-tab’ are displayed in the yellow text field of the main window when the mouse pointer enters the cell.
New in DiscretePath 2.2.5 (Jun 20, 2022)
- Improvements:
- The import of data from the clipboard is now much faster (up to 40%).
- A graph can be drawn in ‘full layout’ that is based on drawing the cycles and paths that make up the graph or using the ‘barycenter layout’. The ‘barycenter layout’ is based on the ‘barycenter heuristic and the reorderable matrix’ algorithm (see User’s guide). This results in a simple layout that draws quickly and can reveal other information not visible in the full layout.
- Bug fixes:
- If you press the ‘ESC’ key to stop importing data from the clipboard, the application will no longer crash.
- When closing the application with a blank canvas, the error message that sometimes appeared is no longer displayed.
New in DiscretePath 2.2.0 (Apr 3, 2022)
- Improvements:
- The calculation of the number of crossings in a graph is calculated with a more precise algorithm that is not based on mathematics but on the graphical properties of the graph. This algorithm is especially suitable for smaller graphs. The algorithm used to calculate the number of crossings in a graph is described in: https://www.intrinsic-code.eu/download/the-graph-algorithms-explained/
- The graph properties summary (context menu of the ‘Info’ tab of the Palette window) is more informative.
- Optimization of the calculations of the centralities.
- Optimization of graph redrawing when the properties of a vertex or edge are changed.
- More actions that allow ‘undo/redo’.
- The weight of multiple edges can be set at once in the ‘Layout’ tab of the Palette window.
- Bug fixes:
- Changing the category of one vertex in the ‘Layout’ tab (Palette window) no longer results in a crash.
New in DiscretePath 2.1.5 (Jan 14, 2022)
- Improvements:
- The tool to assign categories to vertices and draw the vertices in their category layout has been expanded and further integrated into the software.
- The textfield of the canvas window is more readable and now shows at the mouse pointer the information of the vertices and edges of the canvas or the entire contents of the cell in the table of the ‘Info’ tab of the Palette window.
- The ‘undo/redo’ has been optimized.
- The efficiency of both the drawing and the calculations has been improved.
- Vertices belonging to the same category are similar to each other based on certain conditions as lipids in biochemistry, and age or gender in social networks.
- Bug fixes:
- When non-existent categories are imported into a graph, these categories are created using the default vertex layout.
- In previous versions, closing the application without opening or drawing a graph resulted in an error message. This error has been resolved.
New in DiscretePath 2.1.4 (Nov 29, 2021)
- Improvements:
- Data can be imported from the clipboard into the graph displayed on the canvas. Until now, only a new graph could be created from data on the clipboard.
- In general, data import is optimized.
- Selecting vertices and edges by mouse dragging is no longer limited by the size of the graph. Selection by mouse dragging was previously only possible on a graph with fewer than 10,000 edges. Although the selection of vertices and edges is no longer limited by the complexity of the graph, selection by mouse dragging shows some delay in large and complex graphs. In general, the selection of multiple vertices and edges in complex graphs is more efficient than in previous versions.
- The code has been optimized and prepared for the next major upgrade (version 2.2.0, release first quarter 2022).
New in DiscretePath 2.1.2 (Oct 11, 2021)
- Improvements:
- After clustering, individual vertices can be assigned to another cluster.
- Interaction between the 'Info' tab of the Palette window and the canvas has been
- More options in the 'contextual menus' and higher reactivity.
- The 'self-loops' (an edge connecting a vertex to itself) of a graph can be selected
- In the canvas as a group and displayed in the 'Info' tab (and removed individually or
- As a group).
- Drawing in the canvas has been improved: stronger anti-aliasing, no red shine on an
- Edge after deselecting, and an optimized refreshing.
- Bug fixes:
- Isolated vertices and leaf vertices containing a self-loop were not always
- Recognized as isolated or leaf vertices, respectively. Isolated vertices with a
- Self-loop were erroneously recognized as leaf vertices. Now all isolated and leaf
- Vertices are recognized correctly.
New in DiscretePath 2.1.0 (Sep 3, 2021)
- Improvements:
- A cluster algorithm based on 'Random walk' is added. This clustering algorithm
- Provides an additional tool to identify clusters of vertices in a graph. Palette
- Window -> tab 'Calculate' -> Section 'Graph clustering'
- In the 'Info' tab, the vertices and edges can always be selected (even if they are
- Shown as a result of a calculation).
- Drawing a graph and organizing the graph into groups and clusters has been further
- Optimized: in the past some drawing combinations were not possible.
- In a 'random walk' without a 'predefined' end point, the weight of the edges can be
- Included in the calculations.
- The random walk algorithm has been improved (better coverage of the graph).
- Bug fixes:
- Occasionally in a random walk, a vertex could be visited twice in a row or an
- Unconnected vertex could be added to the walk.
- In version 2.0.8 selected vertices in the canvas could not be deselected
- Individually by clicking in the selected vertex.
New in DiscretePath 2.0.9 (Sep 1, 2021)
- Improvements:
- A cluster algorithm based on ‘Random walk’ is added. This clustering algorithm provides an additional tool to identify clusters of vertices in a graph. Palette window -> tab ‘Calculate’ -> Section ‘Graph clustering’
- In the ‘Info’ tab, the vertices and edges can always be selected (even if they are shown as a result of a calculation).
- Drawing a graph and organizing the graph into groups and clusters has been further optimized: in the past some drawing combinations were not possible.
- In a ‘random walk’ without a ‘predefined’ end vertex, the weight of the edges can be included in the calculations.
- The random walk algorithm has been improved (better coverage of the graph).
- Bug fixes:
- Occasionally in a random walk, a vertex could be visited twice in a row or an unconnected vertex could be added to the walk.
- In version 2.0.8 selected vertices in the canvas could not be deselected individually by clicking in the selected vertex.
New in DiscretePath 2.0.7 (Aug 9, 2021)
- Improvements:
- When edges are selected in the ‘Info’ tab, only the edges are selected in the graph and not the edges with their connection vertices as before. This allows to remove only the edges and not the connecting vertices.
- Better canvas responsiveness when drawing large charts. When the graph contains more than 10,000 edges, mouse drag selection is blocked: the response time is too slow to be useful and slows down the overall responsiveness of the application.
- Improved overall memory management.
- Bug fixes:
- In version 2.0.6, calculating the s-t minimum cut and the global minimum cut of graphs with less than 7 vertices resulted in an application crash.
- In the previous versions, multiple selection of vertices or edges in the ‘Info’ tab could crash the application in specific cases.
New in DiscretePath 2.0.6 (Jul 6, 2021)
- Important bug fix:
- When the graph was undirected and the edge weight was changed in the Layout tab
- of the Palette window, only one of the directions of the edge was changed in previous
- versions.
- This bug is fixed and now the weights of both directions of the edge are changed
- simultaneously: the weight of the other direction is set to the weight of the
- direction being changed.
- Minor bug fix:
- In the previous version, the smallest global minimum cut was not always shown. This
- error has been fixed.
New in DiscretePath 2.0.5 (Jul 5, 2021)
- Improvements:
- The calculation of the 's-t minimum cut' has been optimized and expanded. The
- Possibility is included to select the minimum cut with the fewest edges or the
- Minimum cut that divides the graph into two parts with as equal a number of vertices
- As possible.
- In the calculation of the global minimum cut, the option is included to omit the
- Leaf vertices, and any newly formed leaf vertices, from the calculation. When the
- Graph contains leaf vertices, the global minimum cut often contains an edge
- Connecting a leaf vertex to the graph. Omitting the leaf vertices from the
- Calculation leads to a a more meaningful result.
- If a larger graph contains edges with negative weight and negative cycles can be
- Formed, the shortest path calculation is still an approximation, but in most cases
- The shortest path calculated is close to the correct solution.
- If a graph contains edges with negative weight, the longest path calculation is
- Still an approximation, but in most cases the longest path calculated is close to the
- Correct solution.
- The interactions with the 'palette window' have been further optimized, such as
- Scrolling and starting calculations.
New in DiscretePath 2.0.4 (Jun 25, 2021)
- Bug fix:
- Version 2.0.3 contained a '.dll file' that was incorrectly recognized by Norton
- Antivirus as a malicious file. This is now solved.
New in DiscretePath 2.0.2 (Jun 23, 2021)
- Improvements:
- If a larger graph contains edges with negative weight and negative cycles can be formed, the shortest path calculation is still an approximation, but in most cases the shortest path calculated is closer to the correct solution than in previous versions.
- If a graph contains edges with negative weight, the longest path calculation is still an approximation, but in most cases the longest path calculated is closer to the correct solution than in previous versions.
- Bug fixes: for the Windows version:
- A mouse click in the canvas while drawing or clustering will no longer crash the application.
- Clicking the ‘Calculating centrality’ or ‘Identify clusters’ pushbuttons in the ‘Calculate’ tab of the Palette window will not cause the scrollbar (and consequently the tab panel) to jump to its ‘start position’.