[XSL-LIST Mailing List Archive Home] [By Thread] [By Date] [Recent Entries] [Reply To This Message]

Re: RDF graph to SVG force-directed layout

Subject: Re: RDF graph to SVG force-directed layout
From: "Michael Kay mike@xxxxxxxxxxxx" <xsl-list-service@xxxxxxxxxxxxxxxxxxxxxx>
Date: Thu, 15 Oct 2020 09:50:42 -0000
Re:  RDF graph to SVG force-directed layout
OK, I'm starting to see where the adjacency logic is, around lines 335-350.

It's computing some kind of "attraction force" for every pair of nodes in the
graph, where the force is negative if the two nodes aren't cconnected.

The connectivity of nodes is unchanged for each iteration, but is being
recomputed on each iteration. If the data that you process on each iteration
is a set of tuples comprising

(node, x, y, list-of-adjacent-nodes)

then you can precompute the list-of-adjacent-nodes (and possibly even
list-of-non-adjacent-nodes) at the start, and only modify x and y each time
round the loop.

It would be nice to find a way of reducing the number of distant non-adjacent
nodes you have to consider as the algorithm converges. Perhaps there is some
threshold where if a non-adjacent node is more than a certain distance away,
you can drop it from the list-of-non-adjacent-nodes that you have to consider
next time around, so that over time, you're only looking at your position
relative to nodes that are nearby?

Michael Kay
Saxonica

> On 15 Oct 2020, at 10:17, Michael Kay mike@xxxxxxxxxxxx
<xsl-list-service@xxxxxxxxxxxxxxxxxxxxxx> wrote:
>
> Having said all this, however, making the inner loop of your algorithm 5
times faster is only going to get you from 5 minutes to 1 minute, and to do
better than that (as Liam points out) you need to improve the algorithm.
>
> Doing a fixed number of iterations (50) seems rather crude; is there some
way you could detect convergence and stop when the results are good enough?
>
> Might there be some way of doing initial placement that's better than just
random positioning? For example, perhaps it's the case that in many datasets,
the order of the input nodes reflects some kind of proximity metric, and
therefore computing an initial position based on position in the input
sequence would give faster convergence.
>
> I haven't really worked out what the criteria are for computing node
proximity. I can't see any logic that decides which nodes you want to be
near.
>
> Michael Kay
> Saxonica
>
>> On 15 Oct 2020, at 09:42, Michael Kay mike@xxxxxxxxxxxx
<mailto:mike@xxxxxxxxxxxx> <xsl-list-service@xxxxxxxxxxxxxxxxxxxxxx
<mailto:xsl-list-service@xxxxxxxxxxxxxxxxxxxxxx>> wrote:
>>
>> This deserves closer study than I have time to give it.
>>
>> From a quick look, my attention is drawn to the template rule on line 312.
>>
>> Firstly, the variable $net is a sequence of elements that are essentially
(x, y) pairs, and my instinct is that using sequence of maps would cut a lot
of node-creation cost (and a bit of number-to-string and string-to-number
conversion). In fact, since you are computing the (x, y) pairs only in order
to then compute the sum of the x's and the sum of the y's, it seems
unneccessary to capture these values in a list in the first place; why not
compute the two totals as you go by using xsl:iterate in place of xsl:for-each
at line 325?
>>
>> Line 313 is
>>
>> <xsl:param name="force-nodes" select="key('nodes', ('circle', 'rect'))"
as="element()*"/>
>>
>> where the key is
>>
>> <xsl:key name="nodes" match="svg:g[svg:circle] | svg:g[svg:rect]"
use="concat(svg:circle/local-name(), svg:rect/local-name())"/>
>>
>> This is going to create a key with a very small number of entries, each
indexing a large number of nodes, and that doesn't feel like an efficient
thing to do.
>>
>> At lines 339 and 343, should the following-sibling calls be limited (using
[1]) to the immediatelty following sibling?
>>
>> At line 343, should the generate-id() comparison be replaced by "is"? (The
XJ compiler does this optimisation for you, XX doesn't).
>>
>> Finally, line 360-366 is a classic case of a subtree copy that's making a
very small change to an existing tree; I've written several papers that
attempt to address the problem that this is very inefficient because it
involves copying the whole tree.
>>
>> You might consider, instead of making incremental modifications to the
attributes of the svg:g elements, maintaining for each of these elements a map
containing the original svg:elements and the latest computed values of the
attributes that are being modified. Changing a single property in a map is
much more efficient that changing a single attribute of an element.
>>
>> This would also address another issue: on each iteration where a node is
repositioned, you're generating an SVG @transform attribute to reflect the new
position, and then on the next iteration, you are parsing this attribute to
compute the current position. Much better, surely, to maintain the actual
coordinates.
>>
>> Michael Kay
>> Saxonica
>>
>>
>>> On 14 Oct 2020, at 22:00, Martynas JuseviD
ius martynas@xxxxxxxxxxxxx
<mailto:martynas@xxxxxxxxxxxxx> <xsl-list-service@xxxxxxxxxxxxxxxxxxxxxx
<mailto:xsl-list-service@xxxxxxxxxxxxxxxxxxxxxx>> wrote:
>>>
>>> Hi,
>>>
>>> could anyone suggest any optimizations to this stylesheet that
>>> transforms a graph encoded as RDF/XML to an SVG directed graph layout:
>>>
https://github.com/AtomGraph/Web-Client/blob/develop/src/main/webapp/static/c
om/atomgraph/client/xsl/converters/RDFXML2SVG.xsl
<https://github.com/AtomGraph/Web-Client/blob/develop/src/main/webapp/static/
com/atomgraph/client/xsl/converters/RDFXML2SVG.xsl>
>>>
>>> Output example: https://twitter.com/namedgraph/status/1316476355874304001
>>>
>>> The problem is that it's quite slow: <100 nodes and 5 steps take a few
>>> minutes running on Saxon-JS 2 in Firefox or Chrome.
>>>
>>> It's based on a paper on force directed layout in XSLT: "GraphML
>>> Transformation":
>>>
http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.182.3680&rep=rep1&ty
pe=pdf#page=58
>>>
>>> The algorithm:
>>> 1. position resource nodes (optionally also literals) randomly.
>>> (TO-DO: position on an ellipse?)
>>> 2. move nodes in a loop using the force-directed algorithm
>>> 3. draw lines between the nodes, calculating the correct intersection
>>> with the node border
>>>
>>> Note: only "flat" RDF/XML (properties grouped into descriptions; no
>>> nesting) is supported. It's called RDFXML_PLAIN in Jena.
>>>
>>> If anyone would like a sample file, I can easily provide :)
>>>
>>>
>>> Martynas
>>> atomgraph.com
>>>
>>
>
> XSL-List info and archive <http://www.mulberrytech.com/xsl/xsl-list>
> EasyUnsubscribe <http://lists.mulberrytech.com/unsub/xsl-list/293509> (by
email <>)

Current Thread

PURCHASE STYLUS STUDIO ONLINE TODAY!

Purchasing Stylus Studio from our online shop is Easy, Secure and Value Priced!

Buy Stylus Studio Now

Download The World's Best XML IDE!

Accelerate XML development with our award-winning XML IDE - Download a free trial today!

Don't miss another message! Subscribe to this list today.
Email
First Name
Last Name
Company
Subscribe in XML format
RSS 2.0
Atom 0.3
Site Map | Privacy Policy | Terms of Use | Trademarks
Free Stylus Studio XML Training:
W3C Member
Stylus Studio® and DataDirect XQuery ™are products from DataDirect Technologies, is a registered trademark of Progress Software Corporation, in the U.S. and other countries. © 2004-2013 All Rights Reserved.