Posts by Mathieu Jacomy

Creator of Gephi (but not lead developer!). Engineer and researcher at Sciences po médialab. I'm specialized in digital methods in social sciences, sometimes called digital sociology or digital humanities.

Improving the Gephi User Experience

This is an effort to rethink the design of Gephi authored by Donato Ricci, co-founder of Density Design and senior designer at the Sciences Po médialab in Paris, and me, creator of Gephi and an engineer at the same lab (note that I am not Mathieu Bastian, our lead developer and actual powerhouse of the project for the past 10 years).

While this text presents possible improvements and practical solutions, it does not address practical considerations of available labor. Also, be aware that this is not a formal roadmap for future releases but rather a way to open the current state of our reflections for brainstorming. So feel free to share your ideas and comments with us.

There are five main categories that structure the improvements that we currently envision:

  • Design strategy: Ensure that a coherent design philosophy is applied across the entirety of the project
  • User interface: Identify and correct user-facing errors
  • Network-focus: Re-focus design and architecture around the network’s position of primary importance
  • Filling in the Gaps: Providing expected functionality
  • Miscellany: Other minor issues

In addition, we have drafted a UI mockup illustrating some of our propositions.

Design strategy

Gephi was built by engineers without a comprehensive design strategy. This situation is fairly common: engineers approach design in an ad-hoc fashion learning by trial and errors and through casual user observation but without a formal user-testing protocol. Should the tool succeed, it is mostly because the utility triumphs over the pain of use. Gephi is an embodiment of this phenomenon in its current state. Some computer scientists may find it simple, partly because using terrible interfaces is a part of their job, but for many users Gephi is confusing. Geeks of a masochistic tendency may love the tool as a result of digital Stockholm Syndrome, but the bulk of users that could benefit from Gephi find it to be confusing and opaque. In our defense, developing desktop applications is heavily constrained and the Java technology was not helping us to overcome this difficulty. What could a designer do to alleviate this situation? Apply a strategy.

A designer does more than treating the symptoms of poor usability; he or she approaches user experience from its fundamentals. Improving Gephi requires rethinking some of its longest standing features from a new standpoint. A design strategy is the solid foundation upon which we build both a satisfying user experience and underlying software architecture.

Our design strategy fits in five basic points: obtaining substantial and organized user feedback, giving Gephi a clear workflow, implementing a facet-oriented interface layout, reordering panels from the user standpoint, and removing unnecessary features. Each point is explained in further detail along with practical guidelines for implementing potential solutions in the future.

User feedback

We cannot build a sustainable user interface without a quantitative measure of user activity. These data are necessary to support and validate design choices. One approach to obtain this information is to log and collect feedback about interface usage.

An optional logger could be implemented in Gephi to allow users to opt-in to the collection of logs in order to improve the software. Data harvesting can be done as a campaign: for example, we may ask some users to activate it for one month to evaluate the usage of a new interface paradigm that we are testing.

A clear workflow

Users need a clear and visible path to start with Gephi, in particular when opening a new file. We need to remove information to allow users focusing on what is important.

Gephi involves not only the software itself, but also the installer, website and documentation. Our ultimate goal is to make the entry process as simple as possible by coordinating these different elements. We begin by focusing here on just the software itself. We propose to consider that there are only two proper ways to enter in Gephi:

  • Opening a file (constructing a network from a pre-generated file)
  • Connecting to a data source (embedded scraper or API connection)

We also need to clarify the roles of the “open” and “import” functions. We have to clarify that:

  • If the user has a file and needs to see it in Gephi, then “Open” is the right answer
  • If the user has an external data source he or she wishes to connect to, there is distinct menu option for this function

Use case: we have observed that some users try to get in Gephi with a table of nodes and a table of links, and do not succeed in finding the right path. The problem there is that it is not explicit that it is necessary to create an empty document, go to the data table, and then import the tables. Since the pattern is “I have files and I want to see them in Gephi”, then the answer should be under the “Open” menu item.

Facet-oriented interface layout

Rethinking overall design has the virtue of allowing for the reorganization of the interface from a user-centric perspective. The current interface relies on the panels system provided by the Netbeans Platform, which provides some beneficial properties for design. We were inspired by Ben Shneiderman’s motto of “overview first, zoom and filter, then details-on-demand” and it has been quite successful. However the different views are not articulated in a coherent way and the features sometimes struggle to find the right place in terms of visibility.

We propose three simple guidelines for a better organization of the panels:

  • The global hierarchy of containers should reflect the generality of the features
  • Some panels are not facet-dependent: they should not change with the facet
  • The network should occupy a single place whatever its facet, since it is always the same object

Panels guidelines

These guidelines have two consequences. First: facet-dependent panels should be contained inside facet-independent panels; which is to say that there is a single container for all facet-dependent features. Second: the facet selector (currently the three tabs on top) has to be inside this container.

We illustrate this with a comparison between a representation of the current layout and a new simplified structure.

Web

Reordering panels from the user standpoint

A part of our design strategy is to reduce visual clutter by grouping panels that are not used simultaneously. Though it is not intuitive, we prioritize separating panels that work well together over grouping similar features. For instance the following panels should be placed in different groups in order to be used combined:

  • Filters + Layout
  • Filters + Partition or Ranking
  • Timeline + almost anything else

With the current panels there are at least three obvious groups: one with filters, another with layout, and the third with the timeline. Generic contextual information is a fourth possible group, but could be placed in a non-intrusive location like the footer. Some panels, like statistics, could theoretically be at home in any group or even as a separate window that could be invoked from a menu.

Collapsing panels concept

Panels and groups of panels create two levels, so the “window” menu should have two levels too.

Removing unnecessary features

Reducing complexity can also be accomplished by removing features. We have detected at least one clear candidate for removal, but we may find more unnecessary complications to remove.

The “preview” panel of Gephi has been increasingly simplified over iterative updates. The goal of this feature is to provide a quick way to export cartographies. Users with competence in design tend to rely on third-party tools that provide finer-grained control over the visualization, like Illustrator and Scriptographer. Thus, the focus in Gephi is to provide a quick way to export images that can be manipulated in other tools.

We propose to further streamline preview functionality by removing some advanced label features: they infrequently used, complicated, and at times internally inconsistent with other preview settings. Furthermore, it is not necessary to facilitate changes to features like label and node size and color when such adjustments can be made much more easily using other tools.

User Interface

Donato Ricci has identified various flaws in the Gephi UI. Fixing them is a priority for the future.

User-centric features: reordering workflow

Users think in terms of results they want to obtain. They have an action in mind and they search how to do it. By displaying features according to their result, we can both improve user orientation and reduce the tool’s learning curve. A few examples of follow.

We propose to aggregate Partition and Ranking under the more accessible term “Appearance”, and to reverse the order of what is asked to the user. The current interface is organized in the following way: if the user has metadata that can rank the nodes then the user can visualize it using different attributes like color and size. The new interface inverts this approach: if the user wants to color nodes then he or she chooses which metadata to use. The panel may progress like a wizard to reduce cognitive load by drawing attention only to information that is necessary for a given step.

Unified panel appearance

Collapsing advanced layout settings

The current design of Gephi does not respect the general principle of drawing attention to information that is commonly used while obscuring information that is infrequently used.

Tools of the Overview: many problems to fix

The small tool buttons on the left side of the overview panel have a number of problems including:

  • Confusing icons that do not easily communicate the use of tools
  • Indistinct icons that do not sufficiently distinguish between different tools
  • Missing tools that are commonly expected

These issues are compounded by evidence that the tools themselves do not provide sufficient utility for common use.

We propose to alleviate some of these shortcomings by putting most of these tools in a collapsed panel and to have a normal panel dedicated to the settings of each tool. We also propose to implement a default tool cursor that draws on common mouse usage paradigms to provide intuitive functionality to users:

  • A click-drag starting on the background (or an edge) of the view makes a rectangle selection
  • A click-drag starting on a node moves this node
  • A click on a node selects the node, the shift key is used for multiple selection
  • A click on the background deselects
  • A set of meta-keys changes the click function, for instance the spacebar to switch to the view-panning tool (i.e. the hand in Photoshop)
  • The secondary-click works the same

Fixing highlight colors

Highlighting works by tweaking colors so that some nodes get more contrast than others. The contrast should depend on the background color, but this is not current implementation. At the very leastthe following should be done:

  • White background: highlighted nodes darker and other nodes lighter
  • Black background: highlighted nodes lighter and other nodes darker

Network-focus

As a network analysis tool, the network itself plays an obvious central role in Gephi. We have explored different ways to incorporate the network into the software’s presentation and have developed some suggestions for modifications that would increase interface coherency.

A different layout for the panels: network as background

In this approach, the network is contained by a “background sheet” and floating panels support functions. Such a philosophy has been successfully implemented in other systems like Photoshop or Google Maps. Using the root panel for the network, like grouping facet-dependent panels, fosters the feeling that we always deal with the same object, the network. This operates on the metaphor that we are always manipulating a primary canvas that consists of the network to be analyzed.

Network as background

Statistics as an invoked panel or window

Statistics tend to be used on demand, and thus do not need to be displayed permanently. Rather, a discrete menu or button could invoke the statistics panel when needed. Removing this visual information leaves more room to focus on what is important, i.e. the network.

Workspaces: more visible, on top

The workspaces need more attention. We propose to show them as tabs on the top of Gephi. It is more natural to have the workspaces above the facet selector in the hierarchy of panels. This is consistent with the prevalence of the “tab” paradigm in the browser space.

Workspaces-on-top

Filling in the Gaps: Providing Expected Functionality

In addition to the different aspects listed above, users need some well-known common features such as an “undo” function, even if they are complex to implement.

History and undo: feasible if limited to network structure

A visible trace of previous steps, like a proverbial breadcrumb trail, provides users with a sense of orientation and confidence when exploring and manipulating data in a speculative fashion. This also accelerates the learning process by alleviating cognitive load by not forcing users to have to remember a series of unfamiliar steps. This works in tandem with an “undo” feature, which facilitates experimentation without fear of permanently corrupting data.

History and Undo are complex to implement and burden the development of plugins and modules as these functions tend to be deeply embedded in a piece of software’s architecture. This partly explains why they are not currently available in Gephi. However a prudent approach in Gephi would be to focus recording and reversal of changes to the structure of the network: Nodes and edges, their attributes (including color, size and coordinates), but not the state of panels such as filters, statistics…

An initial approach would be to cover only a minimal set of modifications of the network structure. The history would then contain information about the type of the modification, but not its exact content nor the way it was done (manually, filter, data table…). For instance:

  • Modifying attribute X for node N / n nodes / all nodes
  • Modifying color / size / position for node N / n nodes / all nodes
  • Adding / removing: node N / n nodes / all nodes
  • Adding / removing: node attribute X / n attributes / all attributes
  • …and the same for links

The history would not include operations such as exporting files, taking screenshots, modification of views, changes to settings, or other changes that did not directly affect the structure of the network

Protecting irreversible operations

Some operations are irreversible: removing nodes, edges and attributes (and possibly more). Because these operations are definitive and may cause the loss of a certain quantity of work, they should be protected. A classical solution is to ask confirmation for any definitive operation. This is a simple guideline but the result is quite user hostile. We propose a better solution, as implemented in Photoshop: when an irreversible operation has been done, when the user tries to save the network the “Save as…” window appears instead and proposes a different name (with a suffix number or “Copy of X”).

Miscellany

A few additional points deserve to be listed, and are done so in no particular order.

Manual versioning

A basic versioning feature would be appreciated: just the opportunity to save with incrementing / adding a number suffix:

  • “My Network.gexf” is saved as “My Network 01.gexf”
  • “My Network 11.gexf” is saved as “My Network 12.gexf”

A common shortcut for this is Ctrl+Alt+S.

Generalizing zoom options (more internal consistency)

We can currently set how the zoom impacts text labels. The same feature would be useful for edges, for instance to keep 1 pixel lines whatever the zoom, as well as for nodes, for instance to keep small points whatever the zoom.

Generalized zoom options

Size nodes according to area

Our eyes perceive areas. Setting a ranking to the diameter of nodes is less intuitive than to apply it to the area of nodes. We propose to offer an option to customize ranking by either diameter or area, but set the default to area.

Removing unnecessary settings about labels

Node labels and edge labels should help the user identifying nodes. However, using the color or size of labels to visualize attributes is confusing. Gephi presently contains settings to manipulate labels in this way, these settings should be removed and replaced with a simpler interface.

UI Mockup sample (work in progress)

We present here a possible approach to integrate some of the different suggestions made in this document. Consider the following image as a way to help imagine the future of the Gephi user experience.

MockupA-01

As we stated earlier, the purpose of this document is to open up the floor to brainstorming ideas about improving the Gephi UX. Please share your ideas in the comments!

PS: Thanks to Niranjan Sivakumar for his excellent proof-reading 🙂

Gephi is asleep and up to awaken

gephi round graph

Gephi has been almost inactive since quite a long time: we did not release, we did not fix issues, we did not post on the blog. This lack of recent updates creates an increasing amount of difficulties, including installing Gephi on a recent Mac computer. A lot of users ask if the project is still alive. We understand why you wonder and decided to write this post to explain where we’re at and provide to the community a preview of what’s next in Gephi’s lifecycle.

In short, Gephi is still alive yet asleep, but its reawakening is in sight. However, a series of issues prevents us from doing better right now.

The ambitious yet incomplete 0.9 release

The next planned release is Gephi 0.9 and promises to be a major release with a complete rewrite of Gephi’s core module. Performance, and especially memory usage for large graphs has been a lingering issue since the first version of the software. As explained in this article written by Mathieu Bastian – Gephi’s lead developer – the solution resides in a more efficient graph structure implementation that we named “GraphStore”. This technology brings many new features and significantly reduces the memory usage but is a large development effort and requires all modules to be adapted. Indeed, the module which stores and manages the graph is pretty much used by every other module (e.g layout, filters, preview etc.).

This work on the core graph module was initiated as part of a larger vision focused towards a 1.0 release, which aims to address a much larger set of problems, missing measures and bugs. As you may know, the current version has a various set of problems. Some issues are preventing the normal use of the software, like the difficulties to install it on a recent Mac OS X (Yosemite and Maverick). Others are incomplete or missing features, such as various user interface design issues or the improper management of categories’ colors. Finally, some internal problems are hidden in the code but nevertheless real. For example, the technology used to code the user interface (Swing) has been replaced by a more modern technology named JavaFX. For the most part, these problems require a deep rework of the code. The good news is that the most difficult part in this 1.0 vision is probably the rewriting of Gephi’s core graph module, which is what the 0.9 version focus on already.

The current 0.9 developments have reached around 80% completion and many modules, but not all, have already been adapted to GraphStore. A stable version can’t be released until this reaches 100% and all the modules are converted to the new core implementation. Other important issues such as installation issues on recent Macs have already been addressed in this development version. Finally, a series of bugs will be fixed along with minor features and improvements. Finishing the last modules and releasing the 0.9 version is our current priority.

Limited resources

Like many other open source projects, Gephi’s development is for the most part unpaid and remains an activity on the side for all contributors. The notable exception is the Google Summer of Code, which sponsored students multiple years in a row to work on the project. Therefore, the project’s progress depends on the contributors’ professional and personal situations. Although individuals are ready and willing, time is limited and there was just not enough of it lately to make significant progress. Mathieu Bastian is Gephi’s architect and has been behind the software’s key iterations since 2007. This time again he holds the keys to its future and has been involved in the GraphStore project. This complex project requires all of his knowledge of Gephi’s code and is hardly a task someone else could do at this point. Therefore, a part of our development depends on his free time, and we accept it. This situation is temporary though. Indeed, Mathieu will eventually obtain more time to conclude the work on the 0.9 release and Gephi’s development will be less dependent on him in the future.

In addition, we are working on stabilizing some resources in the long run, but our strategy requires a readjustment. Gephi needs time and energy from good java developers, clear-minded designers, and seasoned software architects. We have to entice skilled people, support their involvement and get the best from their contributions. We aim to improve the management of our limited workforce to make the development more attractive and dynamic. This evolution is organized by our team but benefits from external support. For instance, the Sciences Po médialab, the institution I belong to, provides resources for organizing the project, rethinking the user interface and some coding. These changes may not be immediately visible but we’re committed for the medium and long term.

What is next

Releasing the Gephi 0.9 version is the immediate next step. This version will include compatibility fixes and the whole new core based on GraphStore. Then, an important project to rework the overall user experience will be kicked off. It requires a technology switch (from Swing to JavaFX) and the overhaul of a majority of the modules but aims to make Gephi simpler and more intuitive to use. We already have a good diagnostic of the user experience issues in Gephi but need to explore different designs. In an upcoming blog post, I will explain our thought process on this topic with the help of Professore Donato Ricci, senior interaction designer. Eventually, the 1.0 version will be worked on and released.

Gephi is almost 10 years old. It is usable but still plagued with many well-known issues. Though sometimes frustrating, it allows users to do incredible things. We think Gephi is still relevant to research, journalism, civil society and more. We are going to give it the renewal it deserves.

Mathieu Jacomy

ForceAtlas2, the new version of our home-brew Layout

The new version of the build-in layout ForceAtlas is now released. It is scaled for small to medium-size graphs, and is adapted to qualitative interpretation of graphs. The equations are the same as ForceAtlas 1, but there are more options and innovative optimizations that make it a very fast layout algorithm.

It is good enough to deal with very small graphs (10 nodes)  and fast enough to spatialize 10,000 nodes graphs in few minutes, with the same quality. If you have time, it can deal with even bigger graphs.

Update Gephi (Help > Check for Updates) to get this new layout.

Force Atlas 2:

  • Is a continuous algorithm, that allows you to manipulate the graph while it is rendering (a classic force-vector, like Fruchterman Rheingold, and unlike OpenOrd)
  • Has a linear-linear model (attraction and repulsion proportional to distance between nodes). The shape of the graph is between Früchterman & Rheingold’s layout and Noack’s LinLog.
  • Features a unique adaptive convergence speed that allows most graphs to converge more efficiently
  • Proposes summarized settings, focused on what impact the shape of the graph (scaling, gravity…). Default speed should be the good one.
  • Now features a Barnes Hut optimization (performance drops less with big graphs)

 

 

Force Atlas 2 features these settings:

  • Scaling: How much repulsion you want. More makes a more sparse graph.
  • Gravity: Attracts nodes to the center. Prevents islands from drifting away.
  • Dissuade Hubs: Distributes attraction along outbound edges. Hubs attract less and thus are pushed to the borders.
  • LinLog mode: Switch ForceAtlas’ model from lin-lin to lin-log (tribute to Andreas Noack). Makes clusters more tight.
  • Prevent Overlap: Use only when spatialized. Should not be used with “Approximate Repulsion”
  • Tolerance (speed): How much swinging you allow. Above 1 discouraged. Lower gives less speed and more precision.
  • Approximate Repulsion: Barnes Hut optimization: n² complexity to n.ln(n) ; allows larger graphs.
  • Approximation: Theta of the Barnes Hut optimization.
  • Edge Weight Influence: How much influence you give to the edges weight. 0 is “no influence” and 1 is “normal”.

 

 

Force Atlas 2 was created by Mathieu Jacomy at the Sciences Po Médialab (Paris), founding member of the Gephi Consortium.