Java applications can be scaled per-application. Edit the execution script:
nano ~/yEd/yEd
The top few lines are:
#!/bin/sh
# Uncomment the following line to override the JVM search sequence
# INSTALL4J_JAVA_HOME_OVERRIDE=
# Uncomment the following line to add additional VM parameters
# INSTALL4J_ADD_VM_PARAMS=
Add the following (the comment was for my benefit):
# 2019-Nov-28 AM: Additional parameters for High DPI scaling
INSTALL4J_ADD_VM_PARAMS=-Dsun.java2d.uiScale=2.0
Play around with the scaling until you like it. I found 2.0 (200%) quite good.
This was tested on 3.19 and 3.19.1.1 (full install) running on Ubuntu 19.04 and 19.10.